title: Development and validation of knowledge, attitude and practice questionnaire for prevention of respiratory tract infections among Malaysian Hajj pilgrims

text: BACKGROUND: Hajj pilgrimage faces numerous challenges including a high prevalence of respiratory tract infection as well as its prevention strategies. The aim of this study was to develop and validate a questionnaire to evaluate knowledge, attitude and practice (KAP) towards respiratory tract infections (RTIs) prevention among Malaysian Hajj pilgrims. METHODS: This study was conducted among Malaysian Umrah pilgrims in Malaysia from Kuala Lumpur and Kelantan. The questionnaire then underwent a series of validation process that included content, face validity and exploratory part. Item response theory (IRT) analysis was utilized for the validation of the knowledge domain. The attitude and practice were validated using the exploratory factor analysis (EFA). RESULTS: The validation process resulted in a questionnaire that comprised of four main sections: demography, knowledge, attitude, and practice. Following IRT analysis of the knowledge domain, all items analyzed were within the acceptable range of difficulty and discrimination. The Kaiser-Meyer-Olkin measure of sampling adequacy (KMO) was 0.72 and 0.84 for attitude and practice domain respectively and Bartlett’s test of Sphericity for both domains were highly significant (P < 0.001). The factor analysis resulted in two factors with total of 12 items in attitude domain, and 2 factors with total of 13 items in the practice domain with satisfactory factor loading (> 0.3). The Cronbach’s alpha for reliability of the knowledge, attitude and practice domains all showed acceptable values of > 0.6 (0.92, 0.77 and 0.85). CONCLUSION: The findings of this validation and reliability study showed that the developed questionnaire had a satisfactory psychometric property for measuring KAP of Malaysian Hajj pilgrims.


title: Intracerebral haemorrhage (ICH) and COVID-19: Clinical characteristics from a case series

text: • We demonstrate five consecutive cases of predominantly lobar COVID-19-associated intracerebral haemorrhage (ICH). • Patients were typically relatively young with a severe, prolonged inflammatory prodrome. • COVID-19-induced endotheliitis/endotheliopathy may underlie associated cerebrovascular events. • For the clinician, anticoagulation decisions must balance risk of thrombosis with risk of haemorrhage.


title: Diagnosis of human respiratory syncytial virus infection using reverse transcription loop-mediated isothermal amplification

text: Abstract Human respiratory syncytial virus (RSV) is a major causative agent of lower respiratory tract infections in children and the elderly. A reverse transcription-loop-mediated isothermal amplification (RT-LAMP) was developed assay to amplify the genome of RSV subgroups A and B, in order to improve current diagnostic methods for RSV infection. The primer sets for RT-LAMP were designed using highly conserved nucleotide sequences in the matrix protein region of subgroups A and B, and were specific for each subgroup. The RT-LAMP efficiency was compared to virus isolation and a commercially available enzyme immunoassay (EIA) for RSV detection (BD Directigen EZ RSV test™), using nasopharyngeal aspirates from 59 children with respiratory tract infections. The RT-LAMP was specific for RSV and could not detect other respiratory pathogens. 61% (36/59) of children were positive by RT-LAMP, 34% (20/59) by viral isolation, and 56% (26/46) by EZ RSV. Of 16 specimens that were negative by both antigen detection and virus isolation, 12.5% (2/16) were RT-LAMP positive. These results suggest that the RT-LAMP is more sensitive than other methods used to detect RSV. The RT-LAMP assay developed in this study may be useful for diagnostic and epidemiological studies of RSV infection.


title: Inhibition of hepatitis C virus infection and expression in vitro and in vivo by recombinant adenovirus expressing short hairpin RNA

text: Background and Aim: We have reported previously that synthetic small interfering RNA (siRNA) and DNA‐based siRNA expression vectors efficiently and specifically suppress hepatitis C virus (HCV) replication in vitro. In this study, we investigated the effects of the siRNA targeting HCV‐RNA in vivo. Methods: We constructed recombinant retrovirus and adenovirus expressing short hairpin RNA (shRNA), and transfected into replicon‐expressing cells in vitro and transgenic mice in vivo. Results: Retroviral transduction of Huh7 cells to express shRNA and subsequent transfection of an HCV replicon into the cells showed that the cells had acquired resistance to HCV replication. Infection of cells expressing the HCV replicon with an adenovirus expressing shRNA resulted in efficient vector delivery and expression of shRNA, leading to suppression of the replicon in the cells by ∼10(−3). Intravenous delivery of the adenovirus expressing shRNA into transgenic mice that can be induced to express HCV structural proteins by the Cre/loxP switching system resulted in specific suppression of virus protein synthesis in the liver. Conclusion: Taken together, our results support the feasibility of utilizing gene targeting therapy based on siRNA and/or shRNA expression to counteract HCV replication, which might prove valuable in the treatment of hepatitis C.


title: Comments on “coinfection of SARS‐CoV‐2 and HIV in a patient in Wuhan city, China”

text: Zhu et al. report in their letter, Co-infection of SARS-CoV-2 and HIV in a patient in Wuhan city, China, a case of COVID19 in an HIV infected patient1 . However, from the details given in the report, there are doubts that this patient is living with HIV, and additional information would be needed to confirm it. In addition, the antiretroviral drug treatment mentioned is not within the standard guidelines for someone infected with HIV. This article is protected by copyright. All rights reserved.


title: Optimal Nutritional Status for a Well-Functioning Immune System Is an Important Factor to Protect against Viral Infections

text: Public health practices including handwashing and vaccinations help reduce the spread and impact of infections. Nevertheless, the global burden of infection is high, and additional measures are necessary. Acute respiratory tract infections, for example, were responsible for approximately 2.38 million deaths worldwide in 2016. The role nutrition plays in supporting the immune system is well-established. A wealth of mechanistic and clinical data show that vitamins, including vitamins A, B(6), B(12), C, D, E, and folate; trace elements, including zinc, iron, selenium, magnesium, and copper; and the omega-3 fatty acids eicosapentaenoic acid and docosahexaenoic acid play important and complementary roles in supporting the immune system. Inadequate intake and status of these nutrients are widespread, leading to a decrease in resistance to infections and as a consequence an increase in disease burden. Against this background the following conclusions are made: (1) supplementation with the above micronutrients and omega-3 fatty acids is a safe, effective, and low-cost strategy to help support optimal immune function; (2) supplementation above the Recommended Dietary Allowance (RDA), but within recommended upper safety limits, for specific nutrients such as vitamins C and D is warranted; and (3) public health officials are encouraged to include nutritional strategies in their recommendations to improve public health.


title: A theoretical investigation of the structure of 2-nitropyridine-N-oxide and the dependency of the NO(2) torsional motion on the applied wavefunction and basis set

text: HF, B3LYP, and MP2 wave functions in combination with Pople 6-31, 6-311 augmented with polarization functions on all atoms and Dunning double- and triple-zeta basis sets have been employed to investigate the structures and torsional potential function of the nitro group in 2-nitropyridine-N-oxide (2-NPO) and a variety of its fluorinated derivatives. The augmentation of the basis sets with diffuse functions showed a marked effect on the profile and barriers of the NO(2) torsional potential. Depending on the applied model chemistry, the heterocyclic ring in some 2-NPOs has proved to be non-planar. The non-planarity of the ring was characterized by Cremer–Pople puckering amplitude Q. The disruption of the ring planarity in some NPOs was accounted for the distinctive reactivity and impact sensitivity of these heterocycles. Consistently, the NBO and the AIM analyses furnished clear evidence for the accentuated weakness of the C–NO(2) bond and provided evidence for the electronic interplay between the NO(2) group, the fluorine substituent and the heterocyclic ring. Deletion of all off-diagonal Fock-matrix elements (NOSTAR) to separate hyperconjugative stabilizing interactions from steric interactions was used. The effect of nitration and fluorination on the aromaticity of the studied 2-NPOs was investigated by using the NICS descriptors NICS(1) and NICS(1)(zz). These NICS indices have shown that the fluorination in para position to the nitro group exhibits the highest degree of aromaticity within the fluorinated 2-NPOs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11224-012-0198-5) contains supplementary material, which is available to authorized users.


title: A Review on SARS-CoV-2 Virology, Pathophysiology, Animal Models, and Anti-Viral Interventions

text: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of CoV disease 2019 (COVID-19) is a highly pathogenic and transmissible CoV that is presently plaguing the global human population and economy. No proven effective antiviral therapy or vaccine currently exists, and supportive care remains to be the cornerstone treatment. Through previous lessons learned from SARS-CoV-1 and MERS-CoV studies, scientific groups worldwide have rapidly expanded the knowledge pertaining to SARS-CoV-2 virology that includes in vitro and in vivo models for testing of antiviral therapies and randomized clinical trials. In the present narrative, we review SARS-CoV-2 virology, clinical features, pathophysiology, and animal models with a specific focus on the antiviral and adjunctive therapies currently being tested or that require testing in animal models and randomized clinical trials.


title: Synthesis of 3-hetarylpyrroles by Suzuki–Miyaura cross-coupling

text: 1-[tert-Butyl(diphenyl)silyl]pyrrol-3-ylboronic acid was obtained from pyrrole in three steps. Its Suzuki–Miyaura cross-coupling with functionalized pyridinyl and pyrimidinyl bromides afforded new promising 3-hetaryl-1H-pyrroles.


title: Microbiological study of patients hospitalized for acute exacerbation of chronic obstructive pulmonary disease (AE-COPD) and the usefulness of analytical and clinical parameters in its identification (VIRAE study)

text: PURPOSE: Respiratory infection is the most common cause for acute exacerbation of chronic obstructive pulmonary disease (AE-COPD). The aim of this work was to study the etiology of the respiratory infection in order to assess the usefulness of the clinical and analytical parameters used for COPD identification. PATIENTS AND METHODS: We included 132 patients over a period of 2 years. The etiology of the respiratory infection was studied by conventional sputum, paired serology tests for atypical bacteria, and viral diagnostic techniques (immunochromatography, immunofluorescence, cell culture, and molecular biology techniques). We grouped the patients into four groups based on the pathogens isolated (bacterial versus. viral, known etiology versus unknown etiology) and compared the groups. RESULTS: A pathogen was identified in 48 patients. The pathogen was identified through sputum culture in 34 patients, seroconversion in three patients, and a positive result from viral techniques in 14 patients. No significant differences in identifying etiology were observed in the clinical and analytical parameters within the different groups. The most cost-effective tests were the sputum test and the polymerase chain reaction. CONCLUSION: Based on our experience, clinical and analytical parameters are not useful for the etiological identification of COPD exacerbations. Diagnosing COPD exacerbation is difficult, with the conventional sputum test for bacterial etiology and molecular biology techniques for viral etiology providing the most profitability. Further studies are necessary to identify respiratory syndromes or analytical parameters that can be used to identify the etiology of new AE-COPD cases without the laborious diagnostic techniques.


title: Sodium selenite suppresses hepatitis B virus transcription and replication in human hepatoma cell lines

text: Hepatitis B virus (HBV) infection is one of the most serious and prevalent health problems worldwide. Current anti‐HBV medications have a number of drawbacks, such as adverse effects and drug resistance; thus, novel potential anti‐HBV reagents are needed. Selenium (Se) has been shown to be involved in both human immunodeficiency virus and hepatitis C virus infections, but its role in HBV infection remains unclear. To address this, sodium selenite (Na(2)SeO(3)) was applied to three HBV cell models: HepG2.2.15 cells, and HuH‐7 cells transfected with either 1.1 or 1.3× HBV plasmids. Cytotoxicity of Na(2)SeO(3) was examined by Cell Counting Kit‐8. Levels of viral antigen expression, transcripts, and encapsidated viral DNA were measured by enzyme‐linked immunosorbent assay, northern blot, and Southern blot, respectively. There was no obvious cytotoxicity in either HepG2.2.15 or HuH‐7 cells with <2.5 µM Na(2)SeO(3). Below this concentration, Na(2)SeO(3) suppressed HBsAg and HBeAg production, HBV transcript level, and amount of genomic DNA in all three tested models, and suppression level was enhanced in line with increases in Na(2)SeO(3) concentration or treatment time. Moreover, the inhibitory effect of Na(2)SeO(3) on HBV replication can be further enhanced by combined treatment with lamivudine, entecavir, or adefovir. Thus, the present study clearly proves that Na(2)SeO(3) suppresses HBV protein expression, transcription, and genome replication in hepatoma cell models in a dose‐ and time‐dependent manner. J. Med. Virol. 88:653–663, 2016. © 2015 Wiley Periodicals, Inc.


title: Obesity and COVID-19: A Fatal Alliance

text: Most people infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV2) are mildly symptomatic while few progress to critical illness and succumb to the infection. The disease severity is seen to be associated with increasing age and underlying comorbid conditions. Obesity, responsible for various metabolic disorders, appears to be a risk factor in determining the severity of infection despite any age group. Though this association is clinically relevant, the mechanisms underlying are not fully elucidated. SARS CoV2 enters host cell via Angiotensin Converting Enzyme 2 receptor, expression of which is upregulated in visceral fat tissue in obese people, underscoring the fact that adipose tissue is a potential reservoir for virus. Adipose tissue is also a source of many proinflammatory mediators and adipokines. High baseline C-Reactive Protein, interleukin 6, hyperleptinemia with Leptin resistance and hypoadiponectinemia associated with obesity explains the preexisting inflammatory state in obese individuals which predisposes them to worse outcomes and fatality.


title: Bat Coronaviruses and Experimental Infection of Bats, the Philippines

text: Fifty-two bats captured during July 2008 in the Philippines were tested by reverse transcription–PCR to detect bat coronavirus (CoV) RNA. The overall prevalence of virus RNA was 55.8%. We found 2 groups of sequences that belonged to group 1 (genus Alphacoronavirus) and group 2 (genus Betacoronavirus) CoVs. Phylogenetic analysis of the RNA-dependent RNA polymerase gene showed that groups 1 and 2 CoVs were similar to Bat-CoV/China/A515/2005 (95% nt sequence identity) and Bat-CoV/HKU9–1/China/2007 (83% identity), respectively. To propagate group 2 CoVs obtained from a lesser dog-faced fruit bat (Cynopterus brachyotis), we administered intestine samples orally to Leschenault rousette bats (Rousettus leschenaulti) maintained in our laboratory. After virus replication in the bats was confirmed, an additional passage of the virus was made in Leschenault rousette bats, and bat pathogenesis was investigated. Fruit bats infected with virus did not show clinical signs of infection.


Further aspects of doxycycline therapy in COVID‐19


title: Recovering full-length viral genomes from metagenomes

text: Infectious disease metagenomics is driven by the question: “what is causing the disease?” in contrast to classical metagenome studies which are guided by “what is out there?” In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.


title: “Pairing assistance”: the effective way to solve the breakdown of health services system caused by COVID-19 pandemic

text: The most terrifying thing about pandemic could be the large number of patients running against the health service system, which causes a serious shortage of health resources, especially medical personnel. Plotting mortality and diagnosis rates against medical staff resources in 16 cities in Hubei Province, where the epidemic was initially concerned and the most severe, shows a significant negative correlation, indicating the critical role of medical staff resources in controlling epidemics. Nevertheless, it is difficult to ensure that there exist enough medical personnel in cities severely hit by the outbreak. China provides solutions by adopting nationwide “pairing assistance” measures with at least one province assisting one city to alleviate pressure in the most severe area. By plotting the number of patients receiving treatment against day, it is clear that implementing “pairing assistance” is a turning point in China’s fight against epidemics.


title: Genetic characterization of bovine coronavirus in Vietnam

text: A maximum clade credibility tree constructed using the full-length spike (S) and hemagglutinin-esterase genes revealed that Vietnamese Bovine coronavirus (BCoV) strains belong to a single cluster (C1); therefore, they might share a common origin with Cuban and Chinese BCoV strains. The omega values of cluster 1 (C1) and cluster 2 (C2) were 0.15734 and 0.11613, respectively, and naive empirical bayes analysis identified two amino acid positions (179 and 501) in the S protein in C1 and three amino acid positions (113, 501, and 525) in that of C2 that underwent positive selection (p > 99%). The evolutionary rate of C1 was estimated to be 7.6206 × 10(−4) substitutions/site/year, and the most recent common ancestor (tMRCA) of Vietnamese BCoVs was estimated to date back to 1962 (95% HPD 1950–1973). The effective population sizes of C1 and C2 underwent a rapid reduction after 2000 and 2004, respectively. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11262-019-01647-1) contains supplementary material, which is available to authorized users.


title: COVID-19 outbreak: Migration, effects on society, global environment and prevention

text: Abstract The COVID-19 pandemic is considered as the most crucial global health calamity of the century and the greatest challenge that the humankind faced since the 2nd World War. In December 2019, a new infectious respiratory disease emerged in Wuhan, Hubei province, China and was named by the World Health Organization as COVID-19 (coronavirus disease 2019). A new class of corona virus, known as SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has been found to be responsible for occurrence of this disease. As far as the history of human civilization is concerned there are instances of severe outbreaks of diseases caused by a number of viruses. According to the report of the World Health Organization (WHO as of April 18 2020), the current outbreak of COVID-19, has affected over 2164111 people and killed more than 146,198 people in more than 200 countries throughout the world. Till now there is no report of any clinically approved antiviral drugs or vaccines that are effective against COVID-19. It has rapidly spread around the world, posing enormous health, economic, environmental and social challenges to the entire human population. The coronavirus outbreak is severely disrupting the global economy. Almost all the nations are struggling to slow down the transmission of the disease by testing & treating patients, quarantining suspected persons through contact tracing, restricting large gatherings, maintaining complete or partial lock down etc. This paper describes the impact of COVID-19 on society and global environment, and the possible ways in which the disease can be controlled has also been discussed therein.


title: Covid-19, child and adolescent mental health – Croatian (in)experience

text: The Covid-19 pandemic has caused unseen socio-economic changes all over the world, where enormous efforts are being made to preserve lives and maintain functional health systems. A secondary concern is to mitigate the severe economic consequences of the crisis. Different approaches have been adopted with varying outcomes and experiences. But regardless of the different approaches taken, one thing is common for all societies during this pandemic: fear and anxiety. This fear extends from concerns about the present situation, for the health and well-being of family members and loved ones from Covid-19 infection, to fears relating to how long the crisis will last, to the potential economic consequences of the pandemic (perhaps not seen in our lifetimes) and the ultimate fear of future uncertainty. Across the world, health systems are being faced with unprecedented challenges. At their core, these challenges are the same: how to beat Covid-19. Certainly, there are differences in how individual systems are organized and how they address the main issues arising from the pandemic while not forgetting the ongoing healthcare needs of the general population. In this paper, we share some perspectives from Croatia regarding Child and Adolescent Mental Health services (CAMHs) in these extraordinary circumstances. We give our personal insights on deficiencies in Child and Adolescent Mental Health Services prior to the arrival of Covid-19, which have contributed to difficulties in mitigating and managing the ongoing crisis.


title: A Tale of Two Viruses: The Distinct Spike Glycoproteins of Feline Coronaviruses

text: Feline coronavirus (FCoV) is a complex viral agent that causes a variety of clinical manifestations in cats, commonly known as feline infectious peritonitis (FIP). It is recognized that FCoV can occur in two different serotypes. However, differences in the S protein are much more than serological or antigenic variants, resulting in the effective presence of two distinct viruses. Here, we review the distinct differences in the S proteins of these viruses, which are likely to translate into distinct biological outcomes. We introduce a new concept related to the non-taxonomical classification and differentiation among FCoVs by analyzing and comparing the genetic, structural, and functional characteristics of FCoV and the FCoV S protein among the two serotypes and FCoV biotypes. Based on our analysis, we suggest that our understanding of FIP needs to consider whether the presence of these two distinct viruses has implications in clinical settings.


title: Safety, Tolerability, and Pharmacokinetics of Remdesivir, an Antiviral for Treatment of COVID‐19, in Healthy Subjects

text: Remdesivir (RDV), a single diastereomeric monophosphoroamidate prodrug that inhibits viral RNA polymerases, has potent in vitro antiviral activity against SARS‐CoV2. RDV received FDA’s emergency use authorization in United States and approval in Japan for treatment of severe COVID‐19 patients. This report describes two phase 1 studies that evaluated the safety and pharmacokinetics (PK) of single escalating and multiple intravenous (IV) doses of RDV (solution or lyophilized formulation) in healthy subjects. Lyophilized formulation was evaluated for potential future use in clinical trials due to its storage stability in resource‐limited settings. All adverse events were Grade 1 or 2 in severity. Overall, RDV exhibited a linear profile following single‐dose IV administration over 2 hours of RDV solution formulation across the dose range of 3 to 225mg. Both lyophilized and solution formulations provided comparable PK parameters. High intracellular concentrations of the active triphosphate (approximately 220 to 370‐ fold higher than the in vitro EC50 against SARS‐CoV‐2 clinical isolate) were achieved following infusion of 75 mg or 150 mg lyophilized formulation over 30 minutes or 2 hours. Following multiple‐doses of RDV 150mg once daily for 7 or 14 days, RDV exhibited a PK profile similar to single‐dose administration. Metabolite GS‐441524 accumulated approximately 1.9‐fold after daily dosing. Overall, RDV exhibited favorable safety and PK profiles that supported once‐daily dosing.


title: The COVID-19 Crisis: An Opportunity to Integrate Food Democracy into Post-Pandemic Food Systems

text: The world economy is sliding yet into another recession (having arguably barely recovered from the previous economic downturn) due to the worldwide pressures and tensions created by the COVID-19 pandemic.(1) With most countries in the world under lockdown (or in similar situations), almost all food is now consumed in the household. Arguably, agricultural producers and the retail industry appear to be the best placed to weather the storm in order to respond to such a change in demand. However, this is overly simplistic. Recent news of empty shelves in supermarkets whilst dairy farmers have been forced to pour milk down the drain have gone viral.


title: Use, adoption, and effectiveness of tippy-tap handwashing station in promoting hand hygiene practices in resource-limited settings: a systematic review

text: BACKGROUND: Tippy-taps are locally made devices for washing hands with running water. They are simple and low-cost, enabling technology that provides adequate water sources, handwashing stations and motivation for people to prioritise handwashing. This systematic review aimed to establish the use, benefits, adoption and effectiveness of enabling technology; tippy-tap handwashing station, in resource-limited settings. METHODS: We systematically searched for articles in the PubMed, EMBASE, PsycINFO, AMED, CINAHL, DOAJ and Google Scholar databases guided by the acceptable best practice developed by the PROSPERO and COCHRANE for systematic search and selection of articles. Search terms such as tippy-taps, enabling technology, hand-washing station, hand-washing behaviour, diarrhoea, respiratory infection, increase handwashing behaviour were used. In addition, a PRISMA flow diagram was used to elaborate on the number of articles retrieved, retained, excluded and reasons for every action. Studies that used tippy-tap hand washing station as a handwashing facility regardless of the design were included in this review. A mixed method appraisal tool was used to appraise studies. RESULTS: Twenty articles met the eligibility criteria. The use of tippy-taps for handwashing by household members or school children was reported by authors of 16 studies, and it ranged from 2.7 to 80%. The availability of tippy-taps increased handwashing and use of soap among participants. Furthermore, the majority of people who were oriented to tippy-taps or recruited to tippy-tap studies built their tippy-tap stations even after the promotional activities or programs had ended. In one study, tippy-taps were reported by participant to be effective in preventing episodes of stomach pain among participants. CONCLUSION: Tippy-tap handwashing station could help in promoting handwashing practice in resource constraint settings. Future studies are needed to evaluate the effectiveness of tippy-tap hand washing station on preventing water and hygiene-related infections.


title: Guidance for evaluating and testing patients for COVID‐19

text: This month's selection provides guidance to evaluate and test patients for COVID‐19.


Disruption of healthcare: Will the COVID pandemic worsen non-COVID outcomes and disease outbreaks?


title: Pneumothorax and mortality in the mechanically ventilated SARS patients: a prospective clinical study

text: INTRODUCTION: Pneumothorax often complicates the management of mechanically ventilated severe acute respiratory syndrome (SARS) patients in the isolation intensive care unit (ICU). We sought to determine whether pneumothoraces are induced by high ventilatory pressure or volume and if they are associated with mortality in mechanically ventilated SARS patients. METHODS: We conducted a prospective, clinical study. Forty-one mechanically ventilated SARS patients were included in our study. All SARS patients were sedated and received mechanical ventilation in the isolation ICU. RESULTS: The mechanically ventilated SARS patients were divided into two groups either with or without pneumothorax. Their demographic data, clinical characteristics, ventilatory variables such as positive end-expiratory pressure, peak inspiratory pressure, mean airway pressure, tidal volume, tidal volume per kilogram, respiratory rate and minute ventilation and the accumulated mortality rate at 30 days after mechanical ventilation were analyzed. There were no statistically significant differences in the pressures and volumes between the two groups, and the mortality was also similar between the groups. However, patients developing pneumothorax during mechanical ventilation frequently expressed higher respiratory rates on admission, and a lower PaO(2)/FiO(2 )ratio and higher PaCO(2 )level during hospitalization compared with those without pneumothorax. CONCLUSION: In our study, the SARS patients who suffered pneumothorax presented as more tachypnic on admission, and more pronounced hypoxemic and hypercapnic during hospitalization. These variables signaled a deterioration in respiratory function and could be indicators of developing pneumothorax during mechanical ventilation in the SARS patients. Meanwhile, meticulous respiratory therapy and monitoring were mandatory in these patients.


title: Viral respiratory infections among Hajj pilgrims in 2013

text: Middle East respiratory syndrome coronavirus (MERS-CoV) has emerged in the Arabian Gulf region, with its epicentre in Saudi Arabia, the host of the ‘Hajj’ which is the world’s the largest mass gathering. Transmission of MERS-CoV at such an event could lead to its rapid worldwide dissemination. Therefore, we studied the frequency of viruses causing influenza-like illnesses (ILI) among participants in a randomised controlled trial at the Hajj 2013. We recruited 1038 pilgrims from Saudi Arabia, Australia and Qatar during the first day of Hajj and followed them closely for four days. A nasal swab was collected from each pilgrim who developed ILI. Respiratory viruses were detected using multiplex RT-PCR. ILI occurred in 112/1038 (11%) pilgrims. Their mean age was 35 years, 49 (44%) were male and 35 (31%) had received the influenza vaccine pre-Hajj. Forty two (38%) pilgrims had laboratory-confirmed viral infections; 28 (25%) rhinovirus, 5 (4%) influenza A, 2 (2%) adenovirus, 2 (2%) human coronavirus OC43/229E, 2 (2%) parainfluenza virus 3, 1 (1%) parainfluenza virus 1, and 2 (2%) dual infections. No MERS-CoV was detected in any sample. Rhinovirus was the commonest cause of ILI among Hajj pilgrims in 2013. Infection control and appropriate vaccination are necessary to prevent transmission of respiratory viruses at Hajj and other mass gatherings.


title: Fall-related attendance and associated hospitalisation of children and adolescents in Hong Kong: a 12-year retrospective study

text: OBJECTIVES: The present study aimed to examine the trends and characteristics of fall-related attendance in accident and emergency department (AED) by injury type and the trend in associated average length of stay (LOS) among children and adolescents in Hong Kong. DESIGN: A retrospective approach was adopted. SETTING: AED, involving all local public emergency departments from 2001 to 2012. PARTICIPANTS: 63 557 subjects aged 0–19 years with fall injury record were included in the analysis. PRIMARY OUTCOME MEASURES: Fall-related injury number and rates were calculated and reported. Poisson and negative binomial regression models were used to study the trends of injury incidence rate at different body regions. RESULTS: AED fall-related attendance rate increased significantly with an annual percentage change of 4.45 (95% CI 3.43 to 5.47%, p<0.0001). The attendance number of male subjects was persistently higher than female subjects. The standardised rate of fracture injury increased by 1.31% (95% CI 0.56 to 2.05%, p<0.0001) and that of non-fracture injury increased by 9.23% (95% CI 7.07 to 11.43%, p<0.0001) annually. Upper limb was the most frequently fractured location. It included forearm/elbow, shoulder/upper arm and wrist/hand with descending order of frequency. On the contrary, head was the most frequent non-fracture location, followed by forearm/elbow. CONCLUSIONS: The rates of fall-related attendance have been increasing and still remain high. There were significant increases in non-fracture injuries. Fractures were most frequently found in the upper extremity of a child while the most common non-fracture location was head. It appears that more efforts should be made and preventive measures should be implemented for children and adolescents in Hong Kong.


title: Phytochemicals from fern species: potential for medicine applications

text: Ferns are an important phytogenetic bridge between lower and higher plants. Historically they have been used in many ways by humans, including as ornamental plants, domestic utensils, foods, and in handicrafts. In addition, they have found uses as medicinal herbs. Ferns produce a wide array of secondary metabolites endowed with different bioactivities that could potentially be useful in the treatment of many diseases. However, there is currently relatively little information in the literature on the phytochemicals present in ferns and their pharmacological applications, and the most recent review of the literature on the occurrence, chemotaxonomy and physiological activity of fern secondary metabolites was published over 20 years ago, by Soeder (Bot Rev 51:442–536, 1985). Here, we provide an updated review of this field, covering recent findings concerning the bioactive phytochemicals and pharmacology of fern species.


title: Activation and maturation of SARS-CoV main protease

text: The worldwide outbreak of the severe acute respiratory syndrome (SARS) in 2003 was due to the transmission of SARS coronavirus (SARS-CoV). The main protease (M(pro)) of SARS-CoV is essential for the viral life cycle, and is considered to be an attractive target of anti-SARS drug development. As a key enzyme for proteolytic processing of viral polyproteins to produce functional non-structure proteins, M(pro) is first auto-cleaved out of polyproteins. The monomeric form of M(pro) is enzymatically inactive, and it is activated through homo-dimerization which is strongly affected by extra residues to both ends of the mature enzyme. This review provides a summary of the related literatures on the study of the quaternary structure, activation, and self-maturation of M(pro) over the past years.


title: Respiratory Viral Infections in Children and Adolescents with Hematological Malignancies

text: BACKGROUND: Despite the introduction of a polymerase chain reaction (PCR) test for the diagnosis of respiratory viral infection (RVI), guidance on the application of this test and the management of RVI in immunocompromised children is lacking. This study evaluated the clinical characteristics of RVI and established strategies for the PCR test in children and adolescents with hematological malignancies. METHODS: This study included children and adolescents with underlying hematological malignancies and respiratory symptoms, in whom a multiplex PCR test was performed. Patients in whom RVI was identified and not identified were categorized into Groups I and II, respectively. Group I was sub-divided into patients with upper and lower respiratory infections. The medical records of the enrolled patients were retrospectively reviewed. RESULTS: A total of 93 respiratory illnesses were included. Group I included 46 (49.5%) cases of RVI, including 31 (67.4%) upper and 15 (32.6%) lower respiratory infections. Rhinovirus (37.0%) was the most common viral pathogen. Significantly more patients in Group I had community-acquired respiratory illnesses (p=0.003) and complained of rhinorrhea (p<0.001) and sputum (p=0.008) than those in Group II. In Group I, significantly more patients with lower respiratory infections had uncontrolled underlying malignancies (p=0.038) and received re-induction or palliative chemotherapy (p=0.006) than those with upper respiratory infections. CONCLUSIONS: A multiplex PCR test should be considered for RVI diagnosis in immunocompromised children and adolescents with respiratory symptoms, especially in those with rhinorrhea or sputum prominent over a cough. The early application of the PCR test in patients with uncontrolled underlying malignancies may improve outcomes.


title: Host Mixing and Disease Emergence

text: Summary Recent cases of emergent diseases have renewed interest in the evolutionary and ecological mechanisms that promote parasite adaptation to novel hosts [1–6]. Crucial to adaptation is the degree of mixing of original, susceptible hosts, and novel hosts. An increase in the frequency of the original host has two opposing effects on adaptation: an increase in the supply of mutant pathogens with improved performance on the novel host [7–9]; and reduced selection to infect novel hosts, caused by fitness costs commonly observed to be associated with host switching [10–17]. The probability of disease emergence will therefore peak at intermediate frequencies of the original host. We tested these predictions by following the evolution of a virus grown under a range of different frequencies of susceptible (original) and resistant (novel) host bacteria. Viruses that evolved to infect resistant hosts were only detected when susceptible hosts were at frequencies between 0.1% and 1%. Subsequent experiments supported the predictions that there was reduced selection and mutation supply at higher and lower frequencies, respectively. These results suggest that adaptation to novel hosts can occur only under very specific ecological conditions, and that small changes in contact rates between host species might help to mitigate disease emergence.


title: Artemisia annua: Trials are needed for COVID‐19

text: In December 2019, a number of pneumonia cases associated with 2019 novel coronavirus occurred in Wuhan, China. Later taxonomist name the virus SARS‐CoV‐2 and disease called COVID‐19. No approved vaccine or treatment are available for this virus. Current technical guide is related to address therapeutic option for SARS‐CoV‐2. COVID‐19 is great challenge for scientist across the globe. Bioactive compound present in Artemisia annua against, hepatitis B virus, bovine viral diarrhea virus, and Epstein–Barr virus. A. annua have shown significant activity against SARS coronavirus that occur in 2002. This agent is cheap and easily available and will be of great value if they have efficacy against SARS‐CoV‐2. Scientific attention is needed toward this agent to address for the treatment of COVID‐19.


title: Severe Human Lower Respiratory Tract Illness Caused by Respiratory Syncytial Virus and Influenza Virus Is Characterized by the Absence of Pulmonary Cytotoxic Lymphocyte Responses

text: Background. Respiratory syncytial virus (RSV) and influenza virus are common causes of infantile lower respiratory tract infection (LRTI). It is widely believed that both viral replication and inappropriately enhanced immune responses contribute to disease severity. In infants, RSV LRTI is known to be more severe than influenza virus LRTI. Methods. We compared cytokines and chemokines in secretions of infants surviving various forms of respiratory illness caused by RSV or influenza viruses, to determine which mediators were associated with more-severe illness. We analyzed lung tissue from infants with fatal cases of RSV and influenza virus LRTI to determine the types of inflammatory cells present. Autopsy tissues were studied for the lymphotoxin granzyme and the apoptosis marker caspase 3. Results. Quantities of lymphocyte-derived cytokines were minimal in secretions from infants with RSV infection. Concentrations of most cytokines were greater in influenza virus, rather than RSV, infection. Lung tissues from infants with fatal RSV and influenza virus LRTI demonstrated an extensive presence of viral antigen and a near absence of CD8-positive lymphocytes and natural killer cells, with marked expression of markers of apoptosis. Conclusions. Severe infantile RSV and influenza virus LRTI is characterized by inadequate (rather than excessive) adaptive immune responses, robust viral replication, and apoptotic crisis.


Abstracts for Supplement


title: Reverse transcription recombinase-aided amplification assay combined with a lateral flow dipstick for detection of avian infectious bronchitis virus

text: The study was conducted to develop a specific, simple, and sensitive method for diagnosis of avian infectious bronchitis virus (IBV). In this experiment, the selected downstream primer was labeled with biotin and the 5' end of RAA probe was labeled with FAM by reverse transcription recombinase-aided amplification (RT-RAA) combined with lateral flow dipstick (LFD). A RT-RAA-LFD assay that could be used for detection of IBV was established after optimization of RT-RAA reaction time, reaction temperature, and primer concentration. This method did not need reverse transcription of IBV template under isothermal condition (37°C), the amplification of target gene fragments could be completed within only 24 min, and the amplification products could be visually observed and determined by LFD within 3 min. The specificity test demonstrated that there was no cross reaction with the nucleic acids of other similar common pathogens. The lowest detectable limit for IBV was 10(2) copies/μL, and this method was 100 times more sensitive than conventional PCR (10(4) copies/μL), as verified by sensitivity test. The results showed that RT-RAA-LFD assay with strong specificity and high sensitivity was simple and easy to operate, and could be used for rapid detection of IBV in clinical diagnosis.


title: SARS-CoV-2 Detection, Viral Load and Infectivity over the Course of an Infection: SARS-CoV-2 Detection, Viral Load and Infectivity

text: OBJECTIVES: To summarise the evidence on the detection pattern and viral load of SARS-CoV-2 over the course of an infection (including any asymptomatic or pre-symptomatic phase), and the duration of infectivity. METHODS: A systematic literature search was undertaken in PubMed, Europe PubMed Central and EMBASE from 30 December 2019 to 12 May 2020. RESULTS: We identified 113 studies conducted in 17 countries. The evidence from upper respiratory tract samples suggests that the viral load of SARS-CoV-2 peaks around symptom onset or a few days thereafter, and becomes undetectable about two weeks after symptom onset; however, viral loads from sputum samples may be higher, peak later and persist for longer. There is evidence of prolonged virus detection in stool samples, with unclear clinical significance. No study was found that definitively measured the duration of infectivity; however, patients may not be infectious for the entire duration of virus detection, as the presence of viral ribonucleic acid may not represent transmissible live virus. CONCLUSION: There is a relatively consistent trajectory of SARS-CoV-2 viral load over the course of COVID-19 from respiratory tract samples, however the duration of infectivity remains uncertain.


Consistency and reliability of COVID-19 projection models as a means to save lives


title: Two novel adenoviruses found in Cave Myotis bats (Myotis velifer) in Oklahoma

text: Bats are carriers of potentially zoonotic viruses, therefore it is crucial to identify viruses currently found in bats to better understand how they are maintained in bat populations and evaluate risks for transmission to other species. Adenoviruses have been previously detected in bats throughout the world, but sampling is still limited. In this study, 30 pooled-guano samples were collected from a cave roost of Myotis velifer in Oklahoma. A portion of the DNA polymerase gene from Adenoviridae was amplified successfully in 18 M. velifer samples; however, DNA sequence was obtained from only 6 of these M. velifer samples. One was collected in October 2016, one in March 2017, and 4 in July 2017. The October and March samples contained viral DNA that was 3.1% different from each other but 33% different than the novel viral sequence found in the July 2017 samples. Phylogenetic analysis of these fragments confirmed our isolates were from the genus Mastadenovirus and had genetic diversity ranging from 20 to 50% when compared to other bat adenoviruses.


title: Respiratory Disease Markers in Porcine Bronchoalveolar Lavage Fluid

text: In bronchoalveolar lavage fluid (BALF) of pigs originating from different herds bacteria, cells and the antibacterial peptide PR‐39 were examined to gain information about the lung health status. In a high health nucleus herd 56% and in low health herds 20–100% of the examined pigs were found positive for potentially pathogenic bacteria. Based on these findings, a novel definition for bacterial respiratory tract disease was established using an 8% cut‐off for the relative number of neutrophils in bronchoscopic and a 40% cut‐off in transtracheal BALF in combination with the occurrence of potentially pathogenic microorganisms. The antibacterial peptide PR‐39 was highly correlated to this definition of respiratory disease. An assessment of the bacteriological respiratory health status appears to be possibly based on the determination of PR‐39 concentrations in BALF using different cut‐off values according to the lavage method (2.5 nM for bronchoscopic and 5 nM for transtracheal BALF).


title: Trends and advances in food analysis by real-time polymerase chain reaction

text: Analyses to ensure food safety and quality are more relevant now because of rapid changes in the quantity, diversity and mobility of food. Food-contamination must be determined to maintain health and up-hold laws, as well as for ethical and cultural concerns. Real-time polymerase chain reaction (RT-PCR), a rapid and inexpensive quantitative method to detect the presence of targeted DNA-segments in samples, helps in determining both accidental and intentional adulterations of foods by biological contaminants. This review presents recent developments in theory, techniques, and applications of RT-PCR in food analyses, RT-PCR addresses the limitations of traditional food analyses in terms of sensitivity, range of analytes, multiplexing ability, cost, time, and point-of-care applications. A range of targets, including species of plants or animals which are used as food ingredients, food-borne bacteria or viruses, genetically modified organisms, and allergens, even in highly processed foods can be identified by RT-PCR, even at very low concentrations. Microfluidic RT-PCR eliminates the separate sample-processing step to create opportunities for point-of-care analyses. We also cover the challenges related to using RT-PCR for food analyses, such as the need to further improve sample handling. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13197-016-2205-0) contains supplementary material, which is available to authorized users.


title: The role of the Asia-Pacific advisory committee on influenza

text: Abstract In recent years it has become clear that a coordinated approach to the promotion of influenza awareness, with the intent to improve the prevention and control of influenza, is needed in the Asia-Pacific region. The APACI was established in early 2002 to address issues relating to influenza and the impact of the disease in Asia. Its members include influenza researchers, and public health and infectious disease experts from countries in the Asia-Pacific region. The committee is a joint initiative of key opinion leaders in the region, supported by four pharmaceutical companies: Aventis Pasteur, Chiron, GlaxoSmithKline and Wyeth. The activities of the APACI are aligned with, and supplemental to, those of the World Health Organization (WHO) for the global control of influenza. The APACI intends to work in cooperation with the WHO to complement its work on influenza surveillance and promote influenza awareness throughout Asia.


title: Description of viral assemblages associated with the Gorgonia ventalina holobiont

text: The diversity and function of viruses in coral holobionts has only recently received attention. The non-reef building gorgonian octocoral, Gorgonia ventalina, is a major constituent of Caribbean reefs. We investigated viral communities associated with G. ventalina tissues to understand their role in gorgonian ecology. Pyrosequencing was used to prepare a total of 514,632 sequence reads of DNA- and RNA-based mixed-community viral genomes (metaviromes). RNA viral assemblages were comprised of primarily unidentifiable reads, with most matching host transcripts and other RNA metaviromes. DNA metaviromes were similar between healthy and diseased tissues and comprised of contiguous sequences (contigs) that matched primarily metazoan and bacterial proteins. Only ~5% of contigs matched viral proteins that were primarily cyanophage and viruses of Chlorella and Ostreococcus. Our results confirm that DNA and RNA viruses comprise a component of the gorgonian holobiont, suggesting that they may play a role in the ecology of G. ventalina.


title: Deaths from COVID-19 in healthcare workers in Italy—What can we learn?

text: This letter examines healthcare worker deaths by category and medical speciality during the COVID-19 emergency in Italy, and underlines factors that may have contributed to the elevated number of fatalities among healthcare personnel. These data are now available because Italy was the first western country to be severely affected. These are matters for urgent discussion as development goes forward.


title: Effectiveness of Patient-Collected Swabs for Influenza Testing

text: OBJECTIVE: To compare the effectiveness of self-collected and health care worker (HCW)–collected nasal swabs for detection of influenza viruses and determine the patients' preference for type of collection. PATIENTS AND METHODS: We enrolled adult patients presenting with influenzalike illness to the Emergency Department at Mayo Clinic, Rochester, Minnesota, from January 28, 2011, through April 30, 2011. Patients self-collected a midturbinate nasal flocked swab from their right nostril following written instructions. A second swab was then collected by an HCW from the left nostril. Swabs were tested for influenza A and B viruses by real-time reverse transcription–polymerase chain reaction, and percent concordance between collection methods was determined. RESULTS: Of the 72 paired specimens analyzed, 25 were positive for influenza A or B RNA by at least one of the collection methods (34.7% positivity rate). When the 14 patients who had prior health care training were excluded, the qualitative agreement between collection methods was 94.8% (55 of 58). Two of the 58 specimens (3.4%) from patients without health care training were positive only by HCW collection, and 1 of 58 (1.7%) was positive only by patient self-collection. A total of 53.4% of patients (31 of 58) preferred the self-collection method over the HCW collection, and 25.9% (15 of 58) had no preference. CONCLUSION: Self-collected midturbinate nasal swabs provide a reliable alternative to HCW collection for influenza A and B virus real-time reverse transcription–polymerase chain reaction.


title: Respiratory viral infections during the 2009–2010 winter season in Central England, UK: incidence and patterns of multiple virus co-infections

text: Acute viral respiratory infections are the most common infections in humans. Co-infection with different respiratory viruses is well documented but not necessarily well understood. The aim of this study was to utilise laboratory data from the winter season following the 2009 influenza A(H1N1) outbreak to investigate rates of respiratory virus co-infections, virus prevalence in different age groups and temporal variations in virus detection. The Health Protection Agency Public Health Laboratory (HPA PHL) Birmingham, UK, routinely uses polymerase chain reaction (PCR) to detect common respiratory viruses. The results from specimens received for respiratory virus investigations from late September 2009 to April 2010 were analysed. A total of 4,821 specimen results were analysed. Of these, 323 (13.2 %) had co-detections of two viruses, 22 (0.9 %) had three viruses and four (0.2 %) had four viruses. Reciprocal patterns of positive or negative associations between different virus pairs were found. Statistical analysis confirmed the significance of negative associations between influenza A and human metapneumovirus (HMPV), and influenza A and rhinovirus. Positive associations between parainfluenza with rhinovirus, rhinovirus with respiratory syncytial virus (RSV) and adenovirus with rhinovirus, parainfluenza and RSV were also significant. Age and temporal distributions of the different viruses were typical. This study found that the co-detection of different respiratory viruses is not random and most associations are reciprocal, either positively or negatively. The pandemic strain of influenza A(H1N1) was notable in that it was the least likely to be co-detected with another respiratory virus.


Common Place for COVID-19 Local Spreading: Observation from Thailand


title: Distinct characteristics of COVID‐19 patients with initial rRT‐PCR‐positive and rRT‐PCR‐negative results for SARS‐CoV‐2

text: Since the coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) first emerged in Wuhan, China in December 2019, the outbreak of COVID-19 epidemic has become an increasingly serious global health concern. Currently, over 150 countries have reported COVID-19 cases, and the situation has progressed to a pandemic associated with substantial morbidity and mortality.1.


title: WHO Paradoxes in Emergency Operations: The Dilemma of a UN Specialized Agency

text: The past two decades have witnessed a major shift in humanitarian operations to respond to more internal conflicts instead of the traditional cross-border wars. Over the recent years, two major shifts have taken place within the WHO to orient toward response to emergencies, namely the introduction of the Humanitarian Reform and the Cluster Approach in 2005 and the introduction of the Emergency Response Framework (ERF). The financing of the agency in humanitarian operations is adding emerging elements to the WHO operations, especially because of the constantly higher contribution from non-state- and state- funding agencies. Pending issues include aspects like health strategy, conflict analysis, legal issues of aid delivery, impartiality in delivering services, and other aspects and needs.


title: In Vitro Bactericidal and Virucidal Efficacy of Povidone-Iodine Gargle/Mouthwash Against Respiratory and Oral Tract Pathogens

text: INTRODUCTION: Recent virus epidemics and rising antibiotic resistance highlight the importance of hygiene measures to prevent and control outbreaks. We investigated the in vitro bactericidal and virucidal efficacy of povidone-iodine (PVP-I) 7% gargle/mouthwash at defined dilution against oral and respiratory tract pathogens. METHODS: PVP-I was tested against Klebsiella pneumoniae and Streptococcus pneumoniae according to bactericidal quantitative suspension test EN13727 and against severe acute respiratory syndrome and Middle East respiratory syndrome coronaviruses (SARS-CoV and MERS-CoV), rotavirus strain Wa and influenza virus A subtype H1N1 according to virucidal quantitative suspension test EN14476. PVP-I 7% gargle/mouthwash was diluted 1:30 with water to a concentration of 0.23% (the recommended concentration for “real-life” use in Japan) and tested at room temperature under clean conditions [0.3 g/l bovine serum albumin (BSA), viruses only] and dirty conditions (3.0 g/l BSA + 3.0 ml/l erythrocytes) as an interfering substance for defined contact times (minimum 15 s). Rotavirus was tested without protein load. A ≥ 5 log(10) (99.999%) decrease of bacteria and ≥ 4 log(10) (99.99%) reduction in viral titre represented effective bactericidal and virucidal activity, respectively, per European standards. RESULTS: PVP-I gargle/mouthwash diluted 1:30 (equivalent to a concentration of 0.23% PVP-I) showed effective bactericidal activity against Klebsiella pneumoniae and Streptococcus pneumoniae and rapidly inactivated SARS-CoV, MERS-CoV, influenza virus A (H1N1) and rotavirus after 15 s of exposure. CONCLUSION: PVP-I 7% gargle/mouthwash showed rapid bactericidal activity and virucidal efficacy in vitro at a concentration of 0.23% PVP-I and may provide a protective oropharyngeal hygiene measure for individuals at high risk of exposure to oral and respiratory pathogens. FUNDING: Mundipharma Research GmbH & Co. KG (MRG).


title: Molecular characterization of type 1 porcine reproductive and respiratory syndrome viruses (PRRSV) isolated in the Netherlands from 2014 to 2016

text: Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of a devastating pig disease present all over the world. The remarkable genetic variation of PRRSV, makes epidemiological and molecular analysis of circulating viruses highly important to review current diagnostic tools and vaccine efficacy. Monitoring PRRS viruses supports modern herd management by explaining the source of found viruses, either internally or externally from the herd. No epidemiological or molecular study has been published on circulating PRRS-viruses in the Netherlands, since the early nineties. Therefore, the objective of this study is to investigate circulating PRRS-viruses in the Netherlands in 2014, 2015 and 2016 on a molecular level by sequencing ORF2, ORF3, ORF4, ORF5, ORF6 and ORF7. The results demonstrate that the 74 PRRSV strains belong to PRRSV-1, but the diversity among strains is high, based on nucleotide identity, individual ORF length and phylogenetic trees of individual ORFs. Furthermore, the data presented here show that the phylogenetic topology of some viruses is ORF dependent and suggests recombination. The identity of the strain of interest might be misinterpreted and wrong conclusions may be drawn in a diagnostic and epidemiological perspective, when only ORF5 is analyzed, as performed in many routine sequencing procedures.


title: Quantify impacted scope of human expired air under different head postures and varying exhalation rates

text: Abstract Many researches indicate human respiration flow and background ventilation are two important aspects leading to possible respiratory disease spread. However, current studies on respiration flow and the resulted exhaled pollutant dispersion are limited, because different head postures, respiration mode, breath rate, room ventilation and so on, can exert profound impacts that are not understood very clearly. To evaluate the role of head postures on transmission of human exhaled pollutants, this study uses a computational fluid dynamics (CFD) program to study the exhalation flow of a sitting adult in a calm indoor office. Four different head postures are considered: sitting upright viewing front, sitting upright but head tilted viewing upward, sitting upright but head turned viewing the lateral, and sitting but pillowing head on a table. Based on the decay percentage of a gas concentration, the impacted scope of expired air is identified. The common posture by sitting upright viewing front is selected to investigate the change of impacted scope with increasing exhalation rates. The experimental test is also carried out using a breathing thermal manikin. This study finds out that the impacted scope of expired air under different head postures is different. The horizontal impacted distance is highly dependent on the specified threshold concentration. If a person sits around at a table and makes a deep exhalation, other people shall be apart from him/her with a larger distance to be free from the exhaled pollutant exposure, once his/her thermal plume is blocked by the table.


title: Short-term forecasting COVID-19 cumulative confirmed cases: Perspectives for Brazil

text: The new Coronavirus (COVID-19) is an emerging disease responsible for infecting millions of people since the first notification until nowadays. Developing efficient short-term forecasting models allow forecasting the number of future cases. In this context, it is possible to develop strategic planning in the public health system to avoid deaths. In this paper, autoregressive integrated moving average (ARIMA), cubist regression (CUBIST), random forest (RF), ridge regression (RIDGE), support vector regression (SVR), and stacking-ensemble learning are evaluated in the task of time series forecasting with one, three, and six-days ahead the COVID-19 cumulative confirmed cases in ten Brazilian states with a high daily incidence. In the stacking-ensemble learning approach, the CUBIST regression, RF, RIDGE, and SVR models are adopted as base-learners and Gaussian process (GP) as meta-learner. The models’ effectiveness is evaluated based on the improvement index, mean absolute error, and symmetric mean absolute percentage error criteria. In most of the cases, the SVR and stacking-ensemble learning reach a better performance regarding adopted criteria than compared models. In general, the developed models can generate accurate forecasting, achieving errors in a range of 0.87%–3.51%, 1.02%–5.63%, and 0.95%–6.90% in one, three, and six-days-ahead, respectively. The ranking of models, from the best to the worst regarding accuracy, in all scenarios is SVR, stacking-ensemble learning, ARIMA, CUBIST, RIDGE, and RF models. The use of evaluated models is recommended to forecasting and monitor the ongoing growth of COVID-19 cases, once these models can assist the managers in the decision-making support systems.


title: On the brighter side of COVID-19 induced Lockdown: Devising the collateral methods to provide Ayurveda consultation during impasse

text: Abstract COVID-19 pandemic and subsequent measures to mitigate it have presented the world with certain unprecedented situations. Lockdown with effective closure of all services including routine health care services has tested the nerves of health care providers for finding novel ways of providing services without getting into the risk of exposure. Telemedicine had been an ideal option for such situations allowing all channels of communication that leverage Information Technology platforms, including voice, audio, text and digital data exchange as a help to diagnosis, prescription and follow up evaluation. Unfortunately this versatility of Telemedicine as a patient –physician interface could not be harnessed well for its technical complexities and unpreparedness of institutions and individuals. Smartphone based video calling using whatsapp messenger has been proposed as a feasible Telemedicine application to provide outpatient services in this scenario. A pilot run of outpatient services during lockdown period through whatsapp facilitated video calling at Ayurveda Gathiya Clinic, State Ayurvedic College and Hospital, Lucknow has shown a way forward of running such services with a mass appeal, ease of operation and high interface gratification among users and service providers. Within its limitations related to the quality and quantity of information sought, this comes as a viable method of patient –physician interfacing during the phase of lockdown.


title: A parallel genome-wide RNAi screening strategy to identify host proteins important for entry of Marburg virus and H5N1 influenza virus

text: BACKGROUND: Genome-wide RNAi screening has been widely used to identify host proteins involved in replication and infection of different viruses, and numerous host factors are implicated in the replication cycles of these viruses, demonstrating the power of this approach. However, discrepancies on target identification of the same viruses by different groups suggest that high throughput RNAi screening strategies need to be carefully designed, developed and optimized prior to the large scale screening. METHODS: Two genome-wide RNAi screens were performed in parallel against the entry of pseudotyped Marburg viruses and avian influenza virus H5N1 utilizing an HIV-1 based surrogate system, to identify host factors which are important for virus entry. A comparative analysis approach was employed in data analysis, which alleviated systematic positional effects and reduced the false positive number of virus-specific hits. RESULTS: The parallel nature of the strategy allows us to easily identify the host factors for a specific virus with a greatly reduced number of false positives in the initial screen, which is one of the major problems with high throughput screening. The power of this strategy is illustrated by a genome-wide RNAi screen for identifying the host factors important for Marburg virus and/or avian influenza virus H5N1 as described in this study. CONCLUSIONS: This strategy is particularly useful for highly pathogenic viruses since pseudotyping allows us to perform high throughput screens in the biosafety level 2 (BSL-2) containment instead of the BSL-3 or BSL-4 for the infectious viruses, with alleviated safety concerns. The screening strategy together with the unique comparative analysis approach makes the data more suitable for hit selection and enables us to identify virus-specific hits with a much lower false positive rate.


title: Nipah Virus: Past Outbreaks and Future Containment

text: Viral outbreaks of varying frequencies and severities have caused panic and havoc across the globe throughout history. Influenza, small pox, measles, and yellow fever reverberated for centuries, causing huge burden for economies. The twenty-first century witnessed the most pathogenic and contagious virus outbreaks of zoonotic origin including severe acute respiratory syndrome coronavirus (SARS-CoV), Ebola virus, Middle East respiratory syndrome coronavirus (MERS-CoV) and Nipah virus. Nipah is considered one of the world’s deadliest viruses with the heaviest mortality rates in some instances. It is known to cause encephalitis, with cases of acute respiratory distress turning fatal. Various factors contribute to the onset and spread of the virus. All through the infected zone, various strategies to tackle and enhance the surveillance and awareness with greater emphasis on personal hygiene has been formulated. This review discusses the recent outbreaks of Nipah virus in Malaysia, Bangladesh and India, the routes of transmission, prevention and control measures employed along with possible reasons behind the outbreaks, and the precautionary measures to be ensured by private–public undertakings to contain and ensure a lower incidence in the future.


title: Analysis of 92 deceased patients with COVID‐19

text: OBJECTIVE: This retrospective study aimed to analysis the clinical characteristics and complications in death cases with novel coronavirus disease‐19 (COVID‐19). METHOD: We collected the medical records of 92 patients with COVID‐19 in Renmin Hospital of Wuhan University who died during January 6th to February 25th, 2020, summarized the clinical characteristics of complications. RESULTS: There were 91 death cases who developed different complications including acute respiratory distress syndrome (ARDS) (73/91), myocardial injury (31/91), liver injury (15/91), renal insufficiency (14/91), multiple organ dysfunction syndrome (MODS) (14/91) and pneumothorax (1/91). Among these patients, 83 patients had at least one complication. While 1 patient who died of recurrent gastrointestinal bleeding was not directly linked to COVID‐19. CONCLUSION: The main complications of deceased patients with COVID‐19 were ARDS, myocardial injury, liver injury, renal insufficiency and MODS. This article is protected by copyright. All rights reserved.


title: Comprehensive review of coronavirus disease 2019 (COVID-19)

text: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in December 2019 in Wuhan, the capital of China's Hubei province and has rapidly spread all over the world. The World Health Organization (WHO) declared the outbreak to be a Public Health Emergency of International Concern on 30 January 2020 and recognized it as a pandemic on 11 March 2020. The number of people diagnosed with COVID-19 worldwide crossed the one million mark on April 2, 2020; two million mark on April 15, 2020; three million mark on April 27,2020 and the four million mark on May 9,2020. Despite containment efforts, more than 187 countries have been affected with more than 4, 178,346 cases in the world with maximum being in USA (1, 347,936) followed by 227,436 in Spain and 224, 422 in United Kingdom as of May, 2020. COVID-19 is the latest threat to face mankind cutting across geographical barriers in a rapidly changing landscape. This review provides an update on a rapidly evolving global pandemic. As we face the threat of emerging and re-emerging infectious diseases, this is a stark reminder to invest in population health, climate change countermeasures, a global health surveillance system and effective research into identifying pathogens, their treatment and prevention and effective health delivery systems.


title: Convalescent patient-derived monoclonal antibodies targeting different epitopes of E protein confer protection against Zika virus in a neonatal mouse model

text: The Zika virus (ZIKV) outbreak and its link to microcephaly triggered a public health concern. To examine antibody response in a patient infected with ZIKV, we used single-cell PCR to clone 31 heavy and light chain-paired monoclonal antibodies (mAbs) that bind to ZIKV envelope (E) proteins isolated from memory B cells of a ZIKV-infected patient. Three mAbs (7B3, 1C11, and 6A6) that showed the most potent and broad neutralization activities against the African, Asian, and American strains were selected for further analysis. mAb 7B3 showed an IC50 value of 11.6 ng/mL against the circulating American strain GZ02. Epitope mapping revealed that mAbs 7B3 and 1C11 targeted residue K394 of the lateral ridge (LR) epitope of the EDIII domain, but 7B3 has a broader LR epitope footprint and recognizes residues T335, G337, E370, and N371 as well. mAb 6A6 recognized residues D67, K118, and K251 of the EDII domain. Interestingly, although the patient was seronegative for DENV infection, mAb 1C11, originating from the VH3-23 and VK1-5 germline pair, neutralized both ZIKV and DENV1. Administration of the mAbs 7B3, 1C11, and 6A6 protected neonatal SCID mice infected with a lethal dose of ZIKV. This study provides potential therapeutic antibody candidates and insights into the antibody response after ZIKV infection.


COVID-19 Precautions: What the MRI Suite Should Know


title: A Practical Approach to the Management of Cancer Patients During the Novel Coronavirus Disease 2019 (COVID‐19) Pandemic: An International Collaborative Group

text: The outbreak of coronavirus disease 2019 (COVID‐19) has rapidly spread globally since being identified as a public health emergency of major international concern and has now been declared a pandemic by the World Health Organization (WHO). In December 2019, an outbreak of atypical pneumonia, known as COVID‐19, was identified in Wuhan, China. The newly identified zoonotic coronavirus, severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2), is characterized by rapid human‐to‐human transmission. Many cancer patients frequently visit the hospital for treatment and disease surveillance. They may be immunocompromised due to the underlying malignancy or anticancer therapy and are at higher risk of developing infections. Several factors increase the risk of infection, and cancer patients commonly have multiple risk factors. Cancer patients appear to have an estimated twofold increased risk of contracting SARS‐CoV‐2 than the general population. With the WHO declaring the novel coronavirus outbreak a pandemic, there is an urgent need to address the impact of such a pandemic on cancer patients. This include changes to resource allocation, clinical care, and the consent process during a pandemic. Currently and due to limited data, there are no international guidelines to address the management of cancer patients in any infectious pandemic. In this review, the potential challenges associated with managing cancer patients during the COVID‐19 infection pandemic will be addressed, with suggestions of some practical approaches. IMPLICATIONS FOR PRACTICE: The main management strategies for treating cancer patients during the COVID‐19 epidemic include clear communication and education about hand hygiene, infection control measures, high‐risk exposure, and the signs and symptoms of COVID‐19. Consideration of risk and benefit for active intervention in the cancer population must be individualized. Postponing elective surgery or adjuvant chemotherapy for cancer patients with low risk of progression should be considered on a case‐by‐case basis. Minimizing outpatient visits can help to mitigate exposure and possible further transmission. Telemedicine may be used to support patients to minimize number of visits and risk of exposure. More research is needed to better understand SARS‐CoV‐2 virology and epidemiology.


title: RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

text: TRIM25 is a novel RNA-binding protein and a member of the Tripartite Motif (TRIM) family of E3 ubiquitin ligases, which plays a pivotal role in the innate immune response. Almost nothing is known about its RNA-related roles in cell biology. Furthermore, its RNA-binding domain has not been characterized. Here, we reveal that RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain, which we postulate to be a novel RNA-binding domain. Using CLIP-seq and SILAC-based co-immunoprecipitation assays, we uncover TRIM25’s endogenous RNA targets and protein binding partners. Finally, we show that the RNA-binding activity of TRIM25 is important for its ubiquitin ligase function. These results reveal new insights into the molecular roles and characteristics of RNA-binding E3 ubiquitin ligases and demonstrate that RNA could be an essential factor for their biological functions.


title: Elevated Plasma Surfactant Protein D (SP‐D) Levels and a Direct Correlation with Anti‐severe Acute Respiratory Syndrome Coronavirus‐specific IgG Antibody in SARS Patients

text: Pulmonary SP‐D is a defence lectin promoting clearance of viral infections. SP‐D is recognized to bind the S protein of SARS‐CoV and enhance phagocytosis. Moreover, systemic SP‐D is widely used as a biomarker of alveolar integrity. We investigated the relation between plasma SP‐D, SARS‐type pneumonia and the SARS‐specific IgG response. Sixteen patients with SARS, 19 patients with community‐acquired pneumonia (CAP) (Streptococcus pneumonia) and 16 healthy control subjects were enrolled in the study. Plasma SP‐D and anti‐SARS‐CoV N protein IgG were measured using ELISA. SP‐D was significantly elevated in SARS‐type pneumonia [median (95% CI), 453 (379–963) ng/ml versus controls 218 (160–362) ng/ml, P < 0.05] like in patients with CAP. SP‐D significantly correlated with anti‐SARS‐CoV N protein IgG (r (2) = 0.5995, P = 0.02). The possible re‐emergence of SARS or SARS‐like infections suggests a need for minimal traumatic techniques for following the alveolar compartment, e.g. during testing of antivirals. We suggest that monitoring systemic SP‐D may be useful in monitoring the alveolar integrity in SARS‐type pneumonia. The significant correlation between plasma SP‐D and anti‐SARS‐CoV‐specific antibodies support the role for SP‐D in interlinking innate and adaptive immune pathways.


title: Bioactive Phytochemical Constituents of Wild Edible Mushrooms from Southeast Asia

text: Mushrooms have a long history of uses for their medicinal and nutritional properties. They have been consumed by people for thousands of years. Edible mushrooms are collected in the wild or cultivated worldwide. Recently, mushroom extracts and their secondary metabolites have acquired considerable attention due to their biological effects, which include antioxidant, antimicrobial, anti-cancer, anti-inflammatory, anti-obesity, and immunomodulatory activities. Thus, in addition to phytochemists, nutritionists and consumers are now deeply interested in the phytochemical constituents of mushrooms, which provide beneficial effects to humans in terms of health promotion and reduction of disease-related risks. In recent years, scientific reports on the nutritional, phytochemical and pharmacological properties of mushroom have been overwhelming. However, the bioactive compounds and biological properties of wild edible mushrooms growing in Southeast Asian countries have been rarely described. In this review, the bioactive compounds isolated from 25 selected wild edible mushrooms growing in Southeast Asia have been reviewed, together with their biological activities. Phytoconstituents with antioxidant and antimicrobial activities have been highlighted. Several evidences indicate that mushrooms are good sources for natural antioxidants and antimicrobial agents


title: A non-invasive method to assess environmental contamination with avian pathogens: beak and feather disease virus (BFDV) detection in nest boxes

text: Indirect transmission of pathogens can pose major risks to wildlife, yet the presence and persistence of wildlife pathogens in the environment has been little studied. Beak and feather disease virus (BFDV) is of global conservation concern: it can infect all members of the Psittaciformes, one of the most threatened bird orders, with infection often being lethal. Indirect transmission of BFDV through contaminated nest hollows has been proposed as a major infection source. However, data on whether and for how long nest sites in the wild remain contaminated have been absent. We determined the BFDV status of birds (parents and nestlings) for 82 nests of Crimson Rosellas, Platycercus elegans and Eastern Rosellas, Platycercus eximius. In 11 of these nests (13.4%, 95% confidence interval 6.9–22.7), we found an infected parent or nestling. Using nest swabs, we then compared BFDV presence at three points in time (before, during and after breeding) in three groups of nest boxes. These were nest boxes occupied by infected birds, and two control groups (nest boxes occupied by uninfected birds, and unoccupied nest boxes). Detection of BFDV on nest swabs was strongly associated with the infection status of parents in each nest box and with the timing of breeding. During breeding, boxes occupied by BFDV-positive birds were significantly more likely to have BFDV-positive nest swabs than boxes occupied by BFDV-negative birds; nest swabs tested BFDV-positive in 80% (28.4–99.5) of nests with parental antigen excretion, 66.7% (9.4–99.2) of nests occupied by parents with BFDV-positive cloacal swabs and 66.7% (22.3–95.7) of nests occupied by parents with BFDV–positive blood. 0% (0–52.2) of nests with BFDV–positive nestlings had BFDV–positive nest swabs. Across all boxes occupied by BFDV-positive birds (parents or nestlings), no nest swabs were BFDV–positive before breeding, 36.4% (95% CI 10.9–69.2) were positive during breeding and 9.1% (0.2–41.3) remained positive after breeding. BFDV was present on nest swabs for up to 3.7 months. Our study provides novel insights into the potential role of nest cavities and other fomites in indirect transmission of BFDV, and possibly other pathogens, and offers a non-invasive method for surveillance of pathogens in wild bird populations.


title: A microsphere-based immunoassay for rapid and sensitive detection of bovine viral diarrhoea virus antibodies

text: Abstract This study describes a novel blocking microsphere-based immunoassay for highly sensitive and specific detection of antibodies against bovine viral diarrhoea virus (BVDV). The intra- and inter-assay variability are 4.9% and less than 7%, respectively, and variability of bead conjugations is less than 6.6%. The diagnostic performance of the assay was evaluated by testing a total of 509 serum samples. Based on a negative/positive cut-off value of 30.3%, the assay has a sensitivity of 99.4% and a specificity of 98.3% relative to ELISA. The new microsphere immunoassay provides an alternative to conventional ELISA systems and can be used for high-throughput screening in the BVD control programmes.


title: Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding

text: The global outbreak of SARS in 2002-2003 was caused by the infection of a new human coronavirus SARS-CoV. The infection of SARS-CoV is mediated mainly through the viral surface glycoproteins, which consist of S1 and S2 subunits and form trimer spikes on the envelope of the virions. Here we report the ectodomain structures of the SARS-CoV surface spike trimer in different conformational states determined by single-particle cryo-electron microscopy. The conformation 1 determined at 4.3 Å resolution is three-fold symmetric and has all the three receptor-binding C-terminal domain 1 (CTD1s) of the S1 subunits in “down” positions. The binding of the “down” CTD1s to the SARS-CoV receptor ACE2 is not possible due to steric clashes, suggesting that the conformation 1 represents a receptor-binding inactive state. Conformations 2-4 determined at 7.3, 5.7 and 6.8 Å resolutions are all asymmetric, in which one RBD rotates away from the “down” position by different angles to an “up” position. The “up” CTD1 exposes the receptor-binding site for ACE2 engagement, suggesting that the conformations 2-4 represent a receptor-binding active state. This conformational change is also required for the binding of SARS-CoV neutralizing antibodies targeting the CTD1. This phenomenon could be extended to other betacoronaviruses utilizing CTD1 of the S1 subunit for receptor binding, which provides new insights into the intermediate states of coronavirus pre-fusion spike trimer during infection.


Letter: The use of Telemedicine by Neurosurgeons during the Covid-era: preliminary results of a cross-sectional research.


title: Chemotactic antiviral cytokines promote infectious apical entry of human adenovirus into polarized epithelial cells

text: Mucosal epithelia provide strong barriers against pathogens. For instance, the outward facing apical membrane of polarized epithelial cells lacks receptors for agents, such as hepatitis C virus, herpesvirus, reovirus, poliovirus or adenovirus. In addition, macrophages eliminate pathogens from the luminal space. Here we show that human adenovirus type 5 engages an antiviral immune response to enter polarized epithelial cells. Blood-derived macrophages co-cultured apically on polarized epithelial cells facilitate epithelial infection. Infection also occurs in the absence of macrophages, if virus-conditioned macrophage-medium containing the chemotactic cytokine CXCL8 (interleukin-8), or recombinant CXCL8 are present. In polarized cells, CXCL8 activates a Src-family tyrosine kinase via the apical CXCR1 and CXCR2 receptors. This activation process relocates the viral co-receptor ανβ3 integrin to the apical surface, and enables apical binding and infection with adenovirus depending on the primary adenovirus receptor CAR. This paradigm may explain how other mucosal pathogens enter epithelial cells. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/ncomms1391) contains supplementary material, which is available to authorized users.


title: Chapter 4 Adolescents and Pets

text: Abstract This chapter describes the multiple stages present during adolescence and the importance of animals in the lives of adolescents. From the ages of 10–25, adolescents and the role that their pets play in each other’s lives change dramatically. Here, we present three adolescent stages and the value of relationships adolescents have with their pets during these distinct stages. How studies have looked at ways pets influence or impact an adolescent’s life will be explored. The chapter also looks more specifically at a pet’s impact on physical health, social-emotional development, and socialization during the adolescence. We examine specific populations of adolescents, such as college students, rural adolescents, homeless adolescents, at-risk adolescents including adolescents who are suicidal, adolescents participating in canine-assisted therapy, and how their pet’s aide the adolescent. Lastly, experiences from several adolescents are provided.


A NEW CHALLENGE FOR CHILD PSYCHIATRISTS: INPATIENT CARE MANAGEMENT DURING CORONAVIRUS PANDEMIC


title: Density of Upper Respiratory Colonization With Streptococcus pneumoniae and Its Role in the Diagnosis of Pneumococcal Pneumonia Among Children Aged <5 Years in the PERCH Study

text: BACKGROUND: Previous studies suggested an association between upper airway pneumococcal colonization density and pneumococcal pneumonia, but data in children are limited. Using data from the Pneumonia Etiology Research for Child Health (PERCH) study, we assessed this potential association. METHODS: PERCH is a case-control study in 7 countries: Bangladesh, The Gambia, Kenya, Mali, South Africa, Thailand, and Zambia. Cases were children aged 1–59 months hospitalized with World Health Organization–defined severe or very severe pneumonia. Controls were randomly selected from the community. Microbiologically confirmed pneumococcal pneumonia (MCPP) was confirmed by detection of pneumococcus in a relevant normally sterile body fluid. Colonization density was calculated with quantitative polymerase chain reaction analysis of nasopharyngeal/oropharyngeal specimens. RESULTS: Median colonization density among 56 cases with MCPP (MCPP cases; 17.28 × 10(6) copies/mL) exceeded that of cases without MCPP (non-MCPP cases; 0.75 × 10(6)) and controls (0.60 × 10(6)) (each P < .001). The optimal density for discriminating MCPP cases from controls using the Youden index was >6.9 log(10) copies/mL; overall, the sensitivity was 64% and the specificity 92%, with variable performance by site. The threshold was lower (≥4.4 log(10) copies/mL) when MCPP cases were distinguished from controls who received antibiotics before specimen collection. Among the 4035 non-MCPP cases, 500 (12%) had pneumococcal colonization density >6.9 log(10) copies/mL; above this cutoff was associated with alveolar consolidation at chest radiography, very severe pneumonia, oxygen saturation <92%, C-reactive protein ≥40 mg/L, and lack of antibiotic pretreatment (all P< .001). CONCLUSIONS: Pneumococcal colonization density >6.9 log(10) copies/mL was strongly associated with MCPP and could be used to improve estimates of pneumococcal pneumonia prevalence in childhood pneumonia studies. Our findings do not support its use for individual diagnosis in a clinical setting.


P.E. Ferguson, N.M. Gilroy, T.P. Sloots, M.D. Nissen, D.E. Dwyer, T.C. Sorrell. Evaluation of a clinical scoring system and directed laboratory testing for respiratory virus infection in hematopoietic stem cell transplant recipients. Transpl Infect Dis 2011: 13: 448–455. xx: 000–000. All rights reserved Abstract: A simple clinical screening (CS) tool for respiratory virus (RV) infection was introduced and evaluated in a single hematology ward, as part of a strategy to reduce nosocomial RV infection. Up to 6 clinical symptoms or signs were scored and a predefined threshold score of ≥2 prompted paired nose/throat swab (NTS) collection for RV testing. The criterion standard for RV infection was positive immunofluorescence (IF) or polymerase chain reaction (PCR) for 7 and 15 viruses, respectively. The tool was shown to be most beneficial at excluding infection at a threshold score of 1 (negative predictive value [NPV] 89%, [95% confidence interval 78–96%], sensitivity 85% [70–94%], specificity 35% [27–43%]), compared with a score of 2 (NPV 85% [76–91%], sensitivity 63% [46–77%], specificity 57% [48–65%]) at a prevalence of 22%. The tool's ability to diagnose infection was limited (positive predictive value 27% and 29% at thresholds 1 and 2). The sensitivity of IF compared with PCR was 45% for the 7 viruses common to both, and 23% for the extended virus panel detected by PCR. An algorithm incorporating CS, paired NTS collection at a threshold of 1 symptom or sign, and sensitive testing including PCR can guide infection control measures in hospitalized hematopoietic stem cell transplant recipients.


title: Synthesis and anti-HIV studies of 2- and 3-adamantyl-substituted thiazolidin-4-ones

text: Abstract A series of novel thiazolidin-4-ones bearing a lipophilic adamantyl substituent at position 2 or 3 were synthesized. A majority of them showed a modest anti-HIV-1 activity, whereas 2-adamantan-1-yl-3-(4,6-dimethylpyrimidin-2-yl)-thiazolidin-4-one (8) was endowed with a remarkable antiviral potency (EC50 =0.67μM). The new series of compounds (22–29) with an adamantyl moiety at the 3-position of the thiazolidinone ring showed good to modest anti-HIV-1 activity (EC50 =1.0–11μM) but also pronounced cytostatic activity. For example 24, 26 and 29 showed an EC50 of 1.0–2.0μM, while the 50% effective concentrations for 23 and 28 were 7.8 and 11.0μM, respectively. X-ray studies and quantum chemical calculations revealed that the anti-HIV activity of the compounds strongly depends on their dipole moments and conformation of the thiazolidinones.


title: Pilot study of influenza vaccine effectiveness in urban Australian children attending childcare

text: Background: Influenza outbreaks in the childcare setting are a significant cause of excess winter morbidity. This study explored methods of follow up and sample collection for a proposed randomised controlled trial of influenza vaccination in children attending childcare. Methods: The study was conducted in four Sydney childcare centres during 2007. Healthy children aged 6–59 months eligible for vaccination were recruited in two centres, with another two acting as controls. Data on influenza‐like illness (ILI: ≥37.8°C plus at least one respiratory symptom) occurrence were collected weekly. In those children with an ILI, parents were asked to collect nasal swabs and send via surface mail for viral polymerase chain reaction. Vaccine efficacy (VE) for ILI was estimated overall and for subgroups aged 6–23 and 24–59 months using the formula VE = 1 − relative risk (RR). Results: Sixty‐three per cent (151/238) of eligible children had parents give consent. Sixty‐three children received influenza vaccine and 88 participated as controls. Of 26 specimens returned, a virus was detected in 18 (69%); none with influenza. Two symptomatic children had positive near‐patient influenza tests in general practice (one a vaccine failure). The RR with 95% confidence interval in all children and those aged 6–23 months were less than one, 0.56 (0.32–1.02) and 0.46 (0.15–1.45), respectively. Conclusions: This study demonstrated the feasibility and utility of parent‐collected and mailed respiratory specimens for VE research in the childcare setting. Two‐thirds of parent‐collected swabs proved positive for at least one virus. Finding ways to reduce reluctance of parents to submit samples could improve the representativeness of samples collected and the power of the study. No evidence was found for influenza VE, but point estimates were in the direction of protection.


title: High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing

text: We have developed a high-resolution genomic mapping technique that combines transposon-mediated insertional mutagenesis with either capillary electrophoresis or massively parallel sequencing to identify functionally important regions of the Venezuelan equine encephalitis virus (VEEV) genome. We initially used a capillary electrophoresis method to gain insight into the role of the VEEV nonstructural protein 3 (nsP3) in viral replication. We identified several regions in nsP3 that are intolerant to small (15 bp) insertions, and thus are presumably functionally important. We also identified nine separate regions in nsP3 that will tolerate small insertions at low temperatures (30°C), but not at higher temperatures (37°C, and 40°C). Because we found this method to be extremely effective at identifying temperature sensitive (ts) mutations, but limited by capillary electrophoresis capacity, we replaced the capillary electrophoresis with massively parallel sequencing and used the improved method to generate a functional map of the entire VEEV genome. We identified several hundred potential ts mutations throughout the genome and we validated several of the mutations in nsP2, nsP3, E3, E2, E1 and capsid using single-cycle growth curve experiments with virus generated through reverse genetics. We further demonstrated that two of the nsP3 ts mutants were attenuated for virulence in mice but could elicit protective immunity against challenge with wild-type VEEV. The recombinant ts mutants will be valuable tools for further studies of VEEV replication and virulence. Moreover, the method that we developed is applicable for generating such tools for any virus with a robust reverse genetics system.


title: Neoplasias hematológicas: interpretación de los hallazgos pulmonares en la tomografía computarizada torácica

text: Resumen La patología pulmonar en la historia de un paciente con neoplasia hematológica es muy frecuente y variable en función de la enfermedad de base y la terapia recibida. La morbimortalidad asociada es alta, por lo que requiere un tratamiento correcto y precoz. La tomografía computarizada (TC) torácica, junto con el análisis de muestras biológicas, son las herramientas de diagnóstico de primera línea empleadas en estos pacientes, y en determinados casos se requieren métodos invasivos. La interpretación de las imágenes exige el análisis de un contexto clínico en muchas ocasiones complejo. Partiendo del conocimiento que adquiere el radiólogo en su formación sobre el diagnóstico diferencial de los hallazgos pulmonares, el objetivo de este trabajo es explicar los aspectos clínicos y radiológicos claves que permiten orientar correctamente el diagnóstico y asimilar el papel actual de la TC en la estrategia terapéutica de este grupo de enfermos. Abstract Lung disease is very common in patients with hematologic neoplasms and varies in function of the underlying disease and its treatment. Lung involvement is associated with high morbidity and mortality, so it requires early appropriate treatment. Chest computed tomography (CT) and the analysis of biologic specimens are the first line diagnostic tools in these patients, and sometimes invasive methods are necessary. Interpreting the images requires an analysis of the clinical context, which is often complex. Starting from the knowledge about the differential diagnosis of lung findings that radiologists acquire during training, this article aims to explain the key clinical and radiological aspects that make it possible to orient the diagnosis correctly and to understand the current role of CT in the treatment strategy for this group of patients.


title: COVID-19 in Italy - Passing through bitter waters

text: The COVID-19 epidemic in Italy has shown many shortcomings of the national health care system but it also represents a historic opportunity to reinforce the central health care governance and reduce inequalities across the country