title: Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins

text: During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand lives. However, the swiftly spreading virus also caused an unprecedentedly rapid response from the research community facing the unknown health challenge of potentially enormous proportions. Unfortunately, the experimental research to understand the molecular mechanisms behind the viral infection and to design a vaccine or antivirals is costly and takes months to develop. To expedite the advancement of our knowledge, we leveraged data about the related coronaviruses that is readily available in public databases and integrated these data into a single computational pipeline. As a result, we provide comprehensive structural genomics and interactomics roadmaps of SARS-CoV-2 and use this information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community.


title: Assessing racial and ethnic disparities using a COVID-19 outcomes continuum for New York State

text: PURPOSE: Heightened COVID-19 mortality among Black non-Hispanic and Hispanic communities (relative to white non-Hispanic) is well established. This study aims to estimate the relative contributions to fatality disparities in terms of differences in SARS-CoV-2 infections, diagnoses, and disease severity. METHODS: We constructed COVID-19 outcome continua (similar to the HIV care continuum) for white non-Hispanic, Black non-Hispanic, and Hispanic adults in New York State. For each stage in the COVID-19 outcome continua (population, infection experience, diagnosis, hospitalization, fatality), we synthesized the most recent publicly-available data. We described each continuum using overall percentages, fatality rates, and relative changes between stages, with comparisons between race and ethnicity using risk ratios. RESULTS: Estimated per-population COVID-19 fatality rates were 0.03%, 0.18%, and 0.12% for white non-Hispanic, Black non-Hispanic, and Hispanic adults. The 3.48-fold disparity for Hispanic, relative to white, communities was explained by differences in infection-experience, whereas the 5.38-fold disparity for non-Hispanic Black, relative to white, communities was primarily driven by differences in both infection-experience and in the need for hospitalization, given infection. CONCLUSIONS: These findings suggest the most impactful stages upon which to intervene with programs and policies to build COVID-19 health equity.


Key Takeaways From the U.S. CDC’s 2019 Antibiotic Resistance Threats Report for Frontline Providers


title: A camel-derived MERS-CoV with a variant spike protein cleavage site and distinct fusion activation properties

text: Middle East respiratory syndrome coronavirus (MERS-CoV) continues to circulate in both humans and camels, and the origin and evolution of the virus remain unclear. Here we characterize the spike protein of a camel-derived MERS-CoV (NRCE-HKU205) identified in 2013, early in the MERS outbreak. NRCE-HKU205 spike protein has a variant cleavage motif with regard to the S2′ fusion activation site—notably, a novel substitution of isoleucine for the otherwise invariant serine at the critical P1′ cleavage site position. The substitutions resulted in a loss of furin-mediated cleavage, as shown by fluorogenic peptide cleavage and western blot assays. Cell–cell fusion and pseudotyped virus infectivity assays demonstrated that the S2′ substitutions decreased spike-mediated fusion and viral entry. However, cathepsin and trypsin-like protease activation were retained, albeit with much reduced efficiency compared with the prototypical EMC/2012 human strain. We show that NRCE-HKU205 has more limited fusion activation properties possibly resulting in more restricted viral tropism and may represent an intermediate in the complex pattern of MERS-CoV ecology and evolution.


title: Understanding the effects of COVID-19 on the health and safety of immigrant hospitality workers in the United States

text: The U.S. tourism and hospitality workforce is disproportionately represented by immigrants and minorities, particularly in low-wage jobs with adverse work conditions. Immigrant hotel and foodservice workers face excess chronic stress and related syndemic risks, exacerbated by social, political, and economic inequities. COVID-19 has suddenly intensified the stressful and already difficult circumstances of immigrant service sector workers. The travel and tourism sector is one of the hardest hit due to widespread travel restrictions and shelter-in-place orders designed to curb infection spread. Restrictions and lockdowns have devastated tourism-dependent destinations and displaced millions of vulnerable workers, causing them to lose their livelihoods. Compared to the general workforce, a sizeable increase in occupational stress has already been observed in the hospitality/tourism sector over the past 15–20 years. COVID-19 and related fears add further strains on immigrant hotel and foodservice workers, potentially exerting a significant toll on mental and physical health and safety.


title: 13 Market Size and Economics for Biosensors

text: Publisher Summary The breadth and depth of biosensor applications have resulted in a 25% increase in the world biosensor market prediction made as early as August 2002 by Kalorama Information for the year 2005 of $2.3 billion to $2.9 billion. Though medical applications remain the major area of application, biosensors are gradually penetrating a wide variety of non-medical areas. Earlier predictions indicated that the medical application was around 90% of the total biosensor market, which includes clinical applications for diabetes, cholesterol, and coagulation monitoring. However, medical applications of biosensors are now down to around 60%. These changes are atributed to the rapidly advancing technologies and to some serious business challenges. The biosensor field has expanded dramatically in the past 45 years or so since the first demonstration of a biosensor application in 1962. Self-diagnosis of blood glucose levels by diabetes sufferers, however, remains the dominant area of biosensor application. The increased investment in new laboratories is essential to permit the application research required for determining the commercial applicability of biosensors. Different trends and models for collaboration between different entities are being noticed at the present time. Some of these trends are presented here. Incubators are springing up wherein scholarly research at universities may be gradually turned into or groomed to becoming successful business ventures. In effect, the future expansion of biosensor markets will depend on the balance between market opportunities and technical and/or financial obstacles. Different examples of biosensor companies along with their product and what analyte it detects have been described. Most, if not all, of the examples have been selected at random to provide an overall perspective of the biosensors that have been or are in the process of being commercialized.


title: Epidemiology of COVID-19 Infection in Oman: Analysis of the First 1304 Cases

text: OBJECTIVES: We sought to identify the epidemiological characteristics of the first case series of patients with COVID-19 in Oman. METHODS: We included national surveillance data of patients with laboratory-confirmed COVID-19 from 24 February to 17 April 2020. Analyses were performed using descriptive and univariate statistics. RESULTS: Of the 1304 patients studied, the mean age was 37.0±13.0 years old, 80.3% were males, and 35.8% were Omanis. The other mostly affected nationalities were Indian (29.1%), Bangladeshi (20.0%), and Pakistani (10.7%). Out of the total, 80.1% were from the Muscat governorate. Omani patients were significantly more likely to be males than females and aged between 20 and 59 years old (p < 0.001). On presentation, 95.9% cases were mild, 3.6% moderate, and 0.5% severe. The case fatality rate was 0.5%. All deaths were from Muscat governorate; four from Mutrah, one from A'Seeb, and one from Bawshar. CONCLUSIONS: This case series provides epidemiological characteristics as well as the early outcomes of patients with laboratory-confirmed COVID-19.


title: Identifying scenarios of benefit or harm from kidney transplantation during the COVID‐19 pandemic: a stochastic simulation and machine learning study

text: Clinical decision‐making in kidney transplantation (KT) during the COVID‐19 pandemic is understandably a conundrum: both candidates and recipients may face increased acquisition risks and case fatality rates (CFRs). Given our poor understanding of these risks, many centers have paused or reduced KT activity, yet data to inform such decisions are lacking. To quantify the benefit/harm of KT in this context, we conducted a simulation study of immediate‐KT vs delay‐until‐after‐pandemic for different patient phenotypes under a variety of potential COVID‐19 scenarios. A calculator was implemented (http://www.transplantmodels.com/covid_sim), and machine learning approaches were used to evaluate the important aspects of our modeling. Characteristics of the pandemic (acquisition risk, CFR) and length of delay (length of pandemic, waitlist priority when modeling deceased donor KT) had greatest influence on benefit/harm. In most scenarios of COVID‐19 dynamics and patient characteristics, immediate‐KT provided survival benefit; KT only began showing evidence of harm in scenarios where CFRs were substantially higher for KT recipients (e.g. ≥50% fatality) than for waitlist registrants. Our simulations suggest that KT could be beneficial in many centers if local resources allow, and our calculator can help identify patients who would benefit most. Furthermore, as the pandemic evolves, our calculator can update these predictions.


title: Ultrastructural changes in the small intestinal epithelium of suckling pigs affected with a transmissible gastroenteritis (TGE)-like disease

text: The small intestine of piglets collected during a sudden outbreak of diarrhoeal disease resembling transmissible gastroenteritis (TGE) was examined by light and electron microscopy. The principal histopathological changes were moderate infiltration by mononuclear cells in the lamina propria of the villi and cytoplasmic vacuolation. These were most pronounced in the epithelial cells covering the villous tips. By scanning electron microscopy, the intestinal villi were swollen and the transverse furrows disappeared. Microvilli were reduced in number leaving denuded areas on the brush border of the villous epithelial cells. The ultrastructural changes were restricted to the cytoplasm of affected villous epithelial cells. The cell organelles were missing in rounded areas leaving cleared areas in the cytoplasm. Parallel fascicles and bundles were seen in these areas. Viral particles with an average diameter of 70 nm were found within the dilated apical tubulo-vesicular system, free in the cytoplasm, among the microvilli or lying free in the intestinal lumen. Viral particles surrounded a non-membrane bound viroplasm in some cases. The negatively stained particles showed a typical coronavirus morphology. These particles were found to be distinct from the known coronaviruses of swine, TGE virus and hemagglutinating encephalomyelitis virus by immune electron microscopy.


title: Respiratory virus infections

text: Summary The respiratory tract is a frequent site of infection with a wide range of viruses. Each family of viruses can cause differing clinical syndromes depending on the age of the patient and the immune response. As a corollary, different clinical syndromes can be caused by different families of viruses.


title: Inhibition of host extracellular signal-regulated kinase (ERK) activation decreases new world alphavirus multiplication in infected cells

text: Abstract New World alphaviruses belonging to the family Togaviridae are classified as emerging infectious agents and Category B select agents. Our study is focused on the role of the host extracellular signal-regulated kinase (ERK) in the infectious process of New World alphaviruses. Infection of human cells by Venezuelan equine encephalitis virus (VEEV) results in the activation of the ERK-signaling cascade. Inhibition of ERK1/2 by the small molecule inhibitor Ag-126 results in inhibition of viral multiplication. Ag-126-mediated inhibition of VEEV was due to potential effects on early and late stages of the infectious process. While expression of viral proteins was down-regulated in Ag-126 treated cells, we did not observe any influence of Ag-126 on the nuclear distribution of capsid. Finally, Ag-126 exerted a broad-spectrum inhibitory effect on New World alphavirus multiplication, thus indicating that the host kinase, ERK, is a broad-spectrum candidate for development of novel therapeutics against New World alphaviruses.


title: Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules?

text: Although proteins have represented the molecular target of choice in the development of new drug candidates, the pharmaceutical importance of ribonucleic acids has gradually been growing. The increasing availability of structural information has brought to light the existence of peculiar three-dimensional RNA arrangements, which can, contrary to initial expectations, be recognized and selectively modulated through small chemical entities or peptides. The application of classical computational methodologies, such as molecular docking, for the rational development of RNA-binding candidates is, however, complicated by the peculiarities characterizing these macromolecules, such as the marked conformational flexibility, the singular charges distribution, and the relevant role of solvent molecules. In this work, we have thus validated and extended the applicability domain of SuMD, an all-atoms molecular dynamics protocol that allows to accelerate the sampling of molecular recognition events on a nanosecond timescale, to ribonucleotide targets of pharmaceutical interest. In particular, we have proven the methodological ability by reproducing the binding mode of viral or prokaryotic ribonucleic complexes, as well as that of artificially engineered aptamers, with an impressive degree of accuracy.


title: Time-to-Death approach in revealing Chronicity and Severity of COVID-19 across the World

text: BACKGROUND: The outbreak of coronavirus disease, 2019 (COVID-19), which started from Wuhan, China, in late 2019, have spread worldwide. A total of 5,91,971 cases and 2,70,90 deaths were registered till 28(th) March, 2020. We aimed to predict the impact of duration of exposure to COVID-19 on the mortality rates increment. METHODS: In the present study, data on COVID-19 infected top seven countries viz., Germany, China, France, United Kingdom, Iran, Italy and Spain, and World as a whole, were used for modeling. The analytical procedure of generalized linear model followed by Gompertz link function was used to predict the impact lethal duration of exposure on the mortality rates. FINDINGS: Of the selected countries and World as whole, the projection based on 21st March, 2020 cases, suggest that a total (95% Cl) of 76 (65–151) days of exposure in Germany, mortality rate will increase by 5 times to 1%. In countries like France and United Kingdom, our projection suggests that additional exposure of 48 days and 7 days, respectively, will raise the mortality rates to10%. Regarding Iran, Italy and Spain, mortality rate will rise to 10% with an additional 3–10 days of exposure. World’s mortality rates will continue increase by 1% in every three weeks. The predicted interval of lethal duration corresponding to each country has found to be consistent with the mortality rates observed on 28th March, 2020. CONCLUSION: The prediction of lethal duration was found to have apparently effective in predicting mortality, and shows concordance with prevailing rates. In absence of any vaccine against COVID-19 infection, the present study adds information about the quantum of the severity and time elapsed to death will help the Government to take necessary and appropriate steps to control this pandemic.


title: Incorporating polymerase chain reaction-based identification, population characterization, and quantification of microorganisms into aerosol science: A review

text: Abstract The quantity, identity, and distribution of biomass in indoor and outdoor aerosols are poorly described. This is not consistent with the current understanding of atmospheric chemistry or the microbiological characterization of aquatic and terrestrial environments. This knowledge gap is due to both difficulties in applying contemporary microbiological techniques to the low biomass concentrations present in aerosols, and the traditional reliance of aerosol researchers on culture-based techniques—the quantitative limitations and ecological biases of which have been well-documented and are now avoided in other environmental matrices. This article reviews the emergence of the polymerase chain reaction (PCR) as a nonculture-based method to determine the identity, distribution, and abundance of airborne microorganisms. To encourage the use of PCR-based techniques by a broad spectrum of aerosol researchers, emphasis is given to the critical, aerosol specific method issues of sample processing, DNA extraction, and PCR inhibition removal. These methods are synthesized into a generalized procedure for the PCR-based study of microbial aerosols—equally applicable to both indoor and outdoor aerosol environments.


title: High speed rail effects on tourism: Spanish empirical evidence derived from China's modelling experience

text: Abstract China and Spain are currently among the top tourist destinations, coming third and fourth place in the 2014 world ranking of tourist arrivals, behind France and the US. Tourism is crucial for the economies of Spain and China, and both countries have the longest high speed rail (HSR) networks in the world. What role has HSR infrastructure played in the development of tourism in both countries? Little research has been done to date, even in Europe, to estimate empirically how tourism indicators are affected by new HSR lines. In 2012 a multivariate panel analysis by Chen and Haynes was applied to 27 Chinese regions, and confirmed that emerging high speed rail services (during the period 1999–2010) had significant positive impacts on boosting tourism in China. No similar empirical tool has ever been tested in Europe. The aim of this paper is to analyse and validate this tool when applied to the Spanish context, and to develop a comparative analysis with the Chinese case study. The methodology is applied to 47 Spanish provinces during the period 1999–2015, and the results clearly reveal a positive but lower-value link (compared to China) between the increase in certain tourism outputs (foreign arrivals and revenues) and HSR network construction. However, further research is needed into the model's limitations, namely the availability of suitable tourism indicators in the official databases, the HSR explanatory variables considered, and the ability to detect “circular cause-effects” between HSR and tourism.


title: Label-free luminescence switch-on detection of hepatitis C virus NS3 helicase activity using a G-quadruplex-selective probe

text: A series of luminescent Ir(iii) complexes were synthesised and evaluated for their ability to act as luminescent G-quadruplex-selective probes. The Ir(iii) complex 9, [Ir(phq)(2)(phen)]PF(6) (where phq = 2-phenylquinoline; phen = 1,10-phenanthroline), exhibited high luminescence in the presence of G-quadruplex DNA compared to dsDNA and ssDNA, and was employed to construct a label-free G-quadruplex-based assay for hepatitis C virus NS3 helicase activity in aqueous solution. Moreover, the application of the assay for screening potential helicase inhibitors was demonstrated. To our knowledge, this is the first G-quadruplex-based assay for helicase activity.


Inflammatory Bowel Disease


title: Emerging Viruses without Borders: The Wuhan Coronavirus

text: The recently emerged coronavirus in Wuhan, China has claimed at least six lives as of January 22 and infected hundreds if not thousands of individuals. The situation has drawn international attention, including from the virology community. We applaud the rapid release to the public of the genome sequence of the new virus by Chinese virologists, but we also believe that increased transparency on disease reporting and data sharing with international colleagues are crucial for curbing the spread of this newly emerging virus to other parts of the world.


title: Natural Bis-Benzylisoquinoline Alkaloids-Tetrandrine, Fangchinoline, and Cepharanthine, Inhibit Human Coronavirus OC43 Infection of MRC-5 Human Lung Cells

text: Stephania tetrandra and other related species of Menispermaceae are the major sources of the bis-benzylisoquinoline alkaloids tetrandrine (TET), fangchinoline (FAN), and cepharanthine (CEP). Although the pharmacological properties of these compounds include anticancer and anti-inflammatory activities, the antiviral effects of these compounds against human coronavirus (HCoV) remain unclear. Hence, the aims of the current study were to assess the antiviral activities of TET, FAN, and CEP and to elucidate the underlying mechanisms in HCoV-OC43-infected MRC-5 human lung cells. These compounds significantly inhibited virus-induced cell death at the early stage of virus infection. TET, FAN, and CEP treatment dramatically suppressed the replication of HCoV-OC43 as well as inhibited viral S and N protein expression. The virus-induced host response was reduced by compound treatment as compared with the vehicle control. Taken together, these findings demonstrate that TET, FAN, and CEP are potential natural antiviral agents for the prevention and treatment of HCoV-OC43 infection.


Patients with COVID-19 and Disguising on Travel History: A Challenge in Disease Screening


title: Clustered airline flight scheduling: Evidence from airline deregulation in Korea

text: Abstract This paper explores the impacts of competition level on airline scheduling in the Korean domestic short-haul routes where a hub-and-spoke system is not the optimal air transport network strategy. The empirical findings using the Korean airline panel data for the period 2006–2010 suggest that competition leads to less differentiated departure flight times as expected from spatial competition theory. Unlike the previous study on the U.S airline industry, the degree of this tendency for less differentiation differs across the type of routes: the Jeju island routes (leisure type) and the inland routes (business type), in the deregulated period. Following the May 2008 Deregulation Act we find an increasingly clustered pattern of airline scheduling in the Jeju island routes where there have been competitive pressures associated with new low cost entrants. This recent evidence would imply that airline carriers strategically schedule departure flight times and allocate flights between routes as competition increases in the deregulated period.


Not Wasting a Crisis: How Geriatrics Clinical Research Can Remain Engaged During COVID‐19


title: Induction of transcription factor Egr-1 gene expression in astrocytoma cells by Murine coronavirus infection

text: Abstract Mouse hepatitis virus (MHV) causes encephalitis and demyelination in the central nervous system (CNS) of susceptible rodents. Astrocytes are one of the major targets for MHV infection in the CNS, and respond to MHV infection by expressing diverse molecules that may contribute to CNS pathogenesis. Here we characterized the activation of an immediate-early transcription factor Egr-1 by MHV infection in an astrocytoma cell line. We found that the expression of Egr-1 was dramatically increased following virus infection. Using various inhibitors of mitogen-activated protein kinases, we identified that the extracellular signal-regulated kinases 1/2 were involved in the activation of Egr-1 transcription by MHV infection. Experiments with ultraviolet light-inactivated virus revealed that the induction of Egr-1 did not require virus replication and was likely mediated during cell entry. We further found that over-expression of Egr-1 suppressed the expression of BNip3, a pro-apoptotic member of the Bcl-2 family. This finding may provide an explanation for our previously observed down-regulation of BNip3 by MHV infection in astrocytoma cells (Cai, Liu, Yu, and Zhang, Virology 316:104–115, 2003). Furthermore, knockdown of Egr-1 by an siRNA inhibited MHV propagation, suggesting the biological relevance of Egr-1 induction to virus replication. In addition, the persistence/demylinating-positive strains (JHM and A59) induced Egr-1 expression, whereas the persistence/demylinating-negative strain (MHV-2) did not. These results indicate a correlation between the ability of MHVs to induce Egr-1 expression and their ability to cause demyelination in the CNS, which may suggest a potential role for the induction of Egr-1 in viral pathogenesis.


title: EGFR as a Negative Regulatory Protein Adjusts the Activity and Mobility of NHE3 in the Cell Membrane of IPEC-J2 Cells With TGEV Infection

text: Transmissible gastroenteritis (TGE) has caused devastating economic losses to the swine industry worldwide, despite extensive research focusing on the pathogenesis of virus infection. The molecular pathogenic mechanism of TGEV-induced diarrhea in piglets is unknown. Intestinal diarrhea is closely related to the function of the Na(+)/H(+) exchanger protein NHE3 in the brush border membrane of small intestine epithelial cells. The epidermal growth factor receptor (EGFR) may act to regulate NHE3 expression. In addition, EGFR may promote viral invasion of host cells. The present study aimed to determine whether NHE3 activity is regulated by altering EGFR expression to affect Na(+) absorption in TGEV-infected intestinal epithelial cells. Porcine intestinal epithelial cells were used as models for TGEV infection. The results showed that Na(+) absorption and NHE3 expression levels decreased in TGEV-infected cells. Proliferation of TGEV within IPEC-J2 cells could be inhibited by treatment with the EGFR inhibitor AG1478 and knockdown; resulting in recovery of Na(+) absorption in TGEV infected cells and increasing the activity and expression of NHE3. Moreover, we demonstrated that NHE3 activity was regulated through the EGFR/ERK pathway. Importantly, NHE3 mobility on the plasma membrane of TGEV infected cells was significantly weaker than that in normal cells, and EGFR inhibition and knockdown recovered this mobility. Our research indicated that NHE3 activity was negatively regulated by EGFR in TGEV-infected intestinal epithelial cells.


$100M in Dislocated Worker grants available


title: Developing a Point-of-Care Molecular Test to Detect SARS-CoV-2

text: There is a need for widespread testing in India to stop the spread of the novel coronavirus in the population. While RT-PCR is the recommended diagnostic technique, its use is limited to well-equipped laboratories due to the need for specialized instrumentation, reagents and trained personnel. Immunodiagnostic tests are not yet recommended by the WHO for diagnosing active infections. There is a strong need for developing point-of-care molecular tests. Based on our past experience with paperfluidic devices for diagnosing bacterial infections by molecular tests, we propose the development of a diagnostic test for COVID-19. As a platform technology, it could be adapted to other viral outbreaks in future.


title: Novel genome polymorphisms in BCG vaccine strains and impact on efficacy

text: Bacille Calmette-Guérin (BCG) is an attenuated strain of Mycobacterium bovis currently used as a vaccine against tuberculosis. Global distribution and propagation of BCG has contributed to the in vitro evolution of the vaccine strain and is thought to partially account for the different outcomes of BCG vaccine trials. Previous efforts by several molecular techniques effectively identified large sequence polymorphisms among BCG daughter strains, but lacked the resolution to identify smaller changes. In this study, we have used a NimbleGen tiling array for whole genome comparison of 13 BCG strains. Using this approach, in tandem with DNA resequencing, we have identified six novel large sequence polymorphisms including four deletions and two duplications in specific BCG strains. Moreover, we have uncovered various polymorphisms in the phoP-phoR locus. Importantly, these polymorphisms affect genes encoding established virulence factors including cell wall complex lipids, ESX secretion systems, and the PhoP-PhoR two-component system. Our study demonstrates that major virulence factors are different among BCG strains, which provide molecular mechanisms for important vaccine phenotypes including adverse effect profile, tuberculin reactivity and protective efficacy. These findings have important implications for the development of a new generation of vaccines.


title: Inhibition of porcine circovirus type 2 replication in mice by RNA interference

text: Abstract Porcine circovirus type 2 (PCV2) is the primary causative agent of an emerging swine disease, postweaning multisystemic wasting syndrome (PMWS) for which no antiviral treatment is available. To exploit the possibility of using RNA interference (RNAi) as a therapeutic approach against the disease, plasmid-borne short hairpin RNAs (shRNAs) were generated to target the PCV2 genome. Transfection of these shRNAs into cultured PK15 cells caused a significant reduction in viral RNA production that was accompanied by inhibiting viral DNA replication and protein synthesis in infected cells. The effect was further tested in vivo in a mouse model that has been developed for PCV2 infection. Mice injected with shRNA before PCV2 infection showed substantially decreased microscopic lesions in inguinal lymph nodes compared to controls. In situ hybridization and immunohistochemical analyses showed that shRNA caused a significant inhibition in the level of viral DNA and protein synthesis detected in the lymph nodes of the treated mice relative to the controls. Taken together, these results indicate that shRNAs are capable of inhibiting PCV2 infection in vitro as well as in vivo and thus may constitute an effective therapeutic strategy for PCV2 infection.


title: Role of viruses in human evolution

text: The study of viral molecular genetics has produced a considerable body of research into the sequences and phylogenetic relationships of human and animal viruses. A review of this literature suggests that humans have been afflicted by viruses throughout their evolutionary history, although the number and types have changed. Some viruses show evidence of long‐standing intimate relationship and cospeciation with hominids, while others are more recently acquired from other species, including African monkeys and apes while our line was evolving in that continent, and domesticated animals and rodents since the Neolithic. Viral selection for specific resistance polymorphisms is unlikely, but in conjunction with other parasites, viruses have probably contributed to selection pressure maintaining major histocompatibility complex (MHC) diversity and a strong immune response. They may also have played a role in the loss in our lineage of N‐glycolylneuraminic acid (Neu5Gc), a cell‐surface receptor for many infectious agents. Shared viruses could have affected hominid species diversity both by promoting divergence and by weeding out less resistant host populations, while viruses carried by humans and other animals migrating out of Africa may have contributed to declines in other populations. Endogenous retroviral insertions since the divergence between humans and chimpanzees were capable of directly affecting hominid evolution through changes in gene expression and development. Yrbk Phys Anthropol 46:14–46, 2003. © 2003 Wiley‐Liss, Inc.


Cancer survivorship care during COVID-19—perspectives and recommendations from the MASCC survivorship study group


Sixty seconds on . . . beards.


title: Current global vaccine and drug efforts against COVID-19: Pros and cons of bypassing animal trials

text: COVID-19 has become one of the biggest health concern, along with huge economic burden. With no clear remedies to treat the disease, doctors are repurposing drugs like chloroquine and remdesivir to treat COVID-19 patients. In parallel, research institutes in collaboration with biotech companies have identified strategies to use viral proteins as vaccine candidates for COVID-19. Although this looks promising, they still need to pass the test of challenge studies in animal models. As various models for SARS-CoV-2 are under testing phase, biotech companies have bypassed animal studies and moved to Phase I clinical trials. In view of the present outbreak, this looks a justified approach, but the problem is that in the absence of animal studies, we can never predict the outcomes in humans. Since animal models are critical for vaccine development and SARS-CoV-2 has different transmission dynamics, in this review we compare different animal models of SARS-CoV-2 with humans for their pathogenic, immune response and transmission dynamics that make them ideal models for vaccine testing for COVID-19. Another issue of using animal model is the ethics of using animals for research; thus, we also discuss the pros and cons of using animals for vaccine development studies.


title: Lockdown of an Orthopedic Department during COVID-19 Epidemics, Our Experience in a General Hospital

text: The COVID-19 disease is rapidly spreading around the world, affecting many countries and their healthcare systems Like many other countries, Iran is struggling with the current situation In this article, we aim to share our perspectives on confronting obstacles mentioned above using appropriate hospital protocols during the COVID-19 crisis We investigated and compared the number of referred patients to the emergency room, elective, and emergent orthopedic operations in our hospital, along with a number of residents and faculty participants in the morning reports and virtual classes before and after the outbreak of COVID-19 in our hospital The number of referred patients to the emergency room was significantly reduced;the number of orthopedic operations was also decreased to almost zero in March 2020 Meanwhile, we managed to dismiss our residents and reduce the number of in-hospital morning reports and conferences Instead, we designed virtual classes, and the number of participants in our virtual classes grew to almost two-third of the whole participant We also managed to fortify our virtual office system to reduce the number of in-hospital visits Since our hospital had become a leading center for the treatment of COVID-19 patients, and the number of referred trauma patients, elective, and trauma operations, along with educational activities, was reduced There was also a significant concern about the management of elective, trauma, and post-operative patients in this era Orthopedic faculty members needed to react to the current situation cautiously We were able to manage the situation with consideration of our educational path, along with the management of personal protective equipment (PPE), and the use of communication technologies and specific protocols to overcome the obstacles mentioned above Yet involved our staff and With orthopedic faculties active involvement at in-hospital activitie and establishment of hospital protocols considering technological facilities and WHO guidelines, we can improve education, management of PPE, and both orthopedic elective and trauma patients


COVID-19-Patienten schon zweieinhalb Tage vor Symptombeginn infektiös


title: Nonconventional opponents: a review of malaria and leishmaniasis among United States Armed Forces

text: As the United States military engage with different countries and cultures throughout the world, personnel become exposed to new biospheres as well. There are many infectious pathogens that are not endemic to the US, but two of particular importance are Plasmodium and Leishmania, which respectively cause malaria and leishmaniasis. These parasites are both known to cause significant disease burden in their endemic locales, and thus pose a threat to military travelers. This review introduces readers to basic life cycle and disease mechanisms for each. Local and military epidemiology are described, as are the specific actions taken by the US military for prevention and treatment purposes. Complications of such measures with regard to human health are also discussed, including possible chemical toxicities. Additionally, poor recognition of these diseases upon an individual’s return leading to complications and treatment delays in the United States are examined. Information about canine leishmaniasis, poorly studied relative to its human manifestation, but of importance due to the utilization of dogs in military endeavors is presented. Future implications for the American healthcare system regarding malaria and leishmaniasis are also presented.


title: Exposures Before Issuance of Stay-at-Home Orders Among Persons with Laboratory-Confirmed COVID-19 — Colorado, March 2020

text: On March 26, 2020, Colorado instituted stay-at-home orders to reduce community transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). To inform public health messaging and measures that could be used after reopening, persons with laboratory-confirmed COVID-19 during March 9-26 from nine Colorado counties comprising approximately 80% of the state's population† (Adams, Arapahoe, Boulder, Denver, Douglas, El Paso, Jefferson, Larimer, and Weld) were asked about possible exposures to SARS-CoV-2 before implementation of stay-at-home orders. Among 1,738 persons meeting the inclusion criteria§ in the Colorado Electronic Disease Surveillance System, 600 were randomly selected and interviewed using a standardized questionnaire by telephone. Data collection during April 10-30 included information about demographic characteristics, occupations, and selected activities in the 2 weeks preceding symptom onset. During the period examined, SARS-CoV-2 molecular testing was widely available in Colorado; community transmission was documented before implementation of the stay-at-home order. At least three attempts were made to contact all selected patients or their proxy (for deceased patients, minors, and persons unable to be interviewed [e.g., those with dementia]) on at least 2 separate days, at different times of day. Data were entered into a Research Electronic Data Capture (version 9.5.13; Vanderbilt University) database, and descriptive analyses used R statistical software (version 3.6.3; The R Foundation).


Gastrointestinal Diseases of the Ferret


"Coping with COVID-19: perspectives of student radiographers"


Moving Beyond Too Little, Too Late: Managing Emerging Infectious Diseases in Wild Populations Requires International Policy and Partnerships


title: A Structured Tool for Communication and Care Planning in the Era of the COVID-19 Pandemic

text: Abstract Residents in long-term care settings are particularly vulnerable to COVID-19 infections and, compared to younger adults, are at higher risk of poor outcomes and death. Given the poor prognosis of resuscitation outcomes for COVID-19 in general, the specter of COVID-19 in long-term care residents should prompt revisiting goals of care. Visitor restriction policies enacted to reduce the risk of transmission of COVID-19 to long-term care residents requires advance care planning discussions to be conducted remotely. A structured approach can help guide discussions regarding the diagnosis, expected course, and care of individuals with COVID-19 in long-term care settings. Information should be shared in a transparent and comprehensive manner to allay the increased anxiety that families may feel during this time. To achieve this, we propose an evidence-based COVID-19 Communication and Care Planning Tool that allows for an informed consent process and shared decision making between the clinician, resident and their family.


title: Human papillomavirus type 16 E6-specific antitumor immunity is induced by oral administration of HPV16 E6-expressing Lactobacillus casei in C57BL/6 mice

text: Given that local cell-mediated immunity (CMI) against the human papillomavirus type 16 E6 (HPV16 E6) protein is important for eradication of HPV16 E6-expressing cancer cells in the cervical mucosa, the HPV16 E6 protein may be a target for the mucosal immunotherapy of cervical cancer. Here, we expressed the HPV16 E6 antigen on Lactobacillus casei (L. casei) and investigated E6-specific CMI following oral administration of the L. casei-PgsA-E6 to mice. Surface expression of HPV16 E6 antigens was confirmed and mice were orally inoculated with the L. casei-PgsA or the L. casei-PgsA-E6. Compared to the L. casei-PgsA-treated mice, significantly higher levels of serum IgG and mucosal IgA were observed in L. casei-PgsA-E6-immunized mice; these differences were significantly enhanced after boost. Consistent with this, systemic and local CMI were significantly increased after the boost, as shown by increased counts of IFN-γ-secreting cells in splenocytes, mesenteric lymph nodes (MLN), and vaginal samples. Furthermore, in the TC-1 tumor model, animals receiving the orally administered L. casei-PgsA-E6 showed reduced tumor size and increased survival rate versus mice receiving control (L. casei-PgsA) immunization. We also found that L. casei-PgsA-E6-induced antitumor effect was decreased by in vivo depletion of CD4(+) or CD8(+) T cells. Collectively, these results indicate that the oral administration of lactobacilli bearing the surface-displayed E6 protein induces T cell-mediated cellular immunity and antitumor effects in mice.


Covid-19: Japan’s success despite inept bureaucracy and incompetence


title: Chapter 3 Preemptive and Proactive Strategies for Food Control and Biosecurity

text: Abstract Food security, sustainable agriculture, and healthy nutrition are the keystones of sustainable development of society that foster the long-lasting well-being of the human population. The global occurrence of exotic diseases, emerging and remerging pathogens, biological weapons, urbanization, and population explosion, decreasing crop yields, climatic changes, biodiversity loss, declining investments, and water scarcity remains a prevalent threat to sustainable agriculture, food security, and control. Proactive and dynamic strategies with stringent biosecurity measures are required to meet the challenge of Sustainable Development Goal 2 “zero hunger” adopted in the year 2015. Lapses in food and agricultural biosecurity measures can have an adverse impact on the health of people and may result in economic chaos. Awareness about biosecurity and bioterrorism has become more critical in recent years as terrorists are becoming more creative in their attack methods and targets. Food biosecurity strategies are essential to protect the food supply from intentional or accidental threats. Industrial and operational designs that inherently support biosecurity procedures should be employed in agriculture and livestock. Food security is a global issue. Substantial progress in food control and biosecurity will be dependent on our technical capacity, dynamic policies, awareness, and a global movement by involving the international regimes based on cooperation and collaboration.


Herpes zoster and severe acute herpetic neuralgia as a complication of COVID-19 infection


title: Lyssaviruses and rabies: current conundrums, concerns, contradictions and controversies

text: Lyssaviruses are bullet-shaped, single-stranded, negative-sense RNA viruses and the causative agents of the ancient zoonosis rabies. Africa is the likely home to the ancestors of taxa residing within the Genus Lyssavirus, Family Rhabdoviridae. Diverse lyssaviruses are envisioned as co-evolving with bats, as the ultimate reservoirs, over seemingly millions of years. In terms of relative distribution, overt abundance, and resulting progeny, rabies virus is the most successful lyssavirus species today, but for unknown reasons. All mammals are believed to be susceptible to rabies virus infection. Besides reservoirs among the Chiroptera, meso-carnivores also serve as major historical hosts and are represented among the canids, raccoons, skunks, mongooses, and ferret badgers. Perpetuating as a disease of nature with the mammalian central nervous system as niche, host breadth alone precludes any candidacy for true eradication. Despite having the highest case fatality of any infectious disease and a burden in excess of or comparative to other major zoonoses, rabies remains neglected. Once illness appears, no treatment is proven to prevent death. Paradoxically, vaccines were developed more than a century ago, but the clear majority of human cases are unvaccinated. Tens of millions of people are exposed to suspect rabid animals and tens of thousands succumb annually, primarily children in developing countries, where canine rabies is enzootic. Rather than culling animal populations, one of the most cost-effective strategies to curbing human fatalities is the mass vaccination of dogs. Building on considerable progress to date, several complementary actions are needed in the near future, including a more harmonized approach to viral taxonomy, enhanced de-centralized laboratory-based surveillance, focal pathogen discovery and characterization, applied pathobiological research for therapeutics, improved estimates of canine populations at risk, actual production of required vaccines and related biologics, strategies to maximize prevention but minimize unnecessary human prophylaxis, and a long-term, realistic plan for sustained global program support to achieve success in disease control, prevention, and elimination.


title: Monoclonal Antibodies and Antibody Like Fragments Derived from Immunised Phage Display Libraries

text: Morbidity and mortality associated with infectious diseases are always on the rise, especially in poorer countries and in the aging population. The inevitable, but unpredictable emergence of new infectious diseases has become a global threat. HIV/AIDS, severe acute respiratory syndrome (SARS), and the more recent H1N1 influenza are only a few of the numerous examples of emerging infectious diseases in the modern era. However despite advances in diagnostics, therapeutics and vaccines, there is need for more specific, efficacious, cost-effective and less toxic treatment and preventive drugs. In this chapter, we discuss a powerful combinatorial technology in association with animal immunisation that is capable of generating biologic drugs with high affinity, efficacy and limited off-site toxicity, and diagnostic tools with great precision. Although time consuming, immunisation still remains the preferred route for the isolation of high-affinity antibodies and antibody-like fragments. Phage display is a molecular diversity technology that allows the presentation of large peptide and protein libraries on the surface of filamentous phage. The selection of binding fragments from phage display libraries has proven significant for routine isolation of invaluable peptides, antibodies, and antibody-like domains for diagnostic and therapeutic applications. Here we highlight the many benefits of combining immunisation with phage display in combating infectious diseases, and how our knowledge of antibody engineering has played a crucial role in fully exploiting these platforms in generating therapeutic and diagnostic biologics towards antigenic targets of infectious organisms.


title: COVID-19: Obstetric anesthesia care considerations

text: • Pre-hospital COVID-19 screening should be implemented for all pregnant patients. • Limit the number of staff in a delivery room or operating room when feasible; • Encourage the use of video messaging with other members of the patient's support system; • An experienced provider should perform neuraxial procedures and intubations, whenever possible.


title: Lupus anticoagulant is frequent in patients with Covid‐19

text: Patients hospitalized for Covid-19 severe infection are more prone to excessive coagulation activation leading to thrombotic events. Tang et al.1 discussed the importance of high D-dimer and Fibrin degradation product level to determine the patient prognostic and the risk of thrombosis. However they did not look at lupus anticoagulant (LAC). Zhang et al. described, three cases of thrombosis associated with antiphospholipid antibodies represented by anticardiolipin (aCL) and anti-β2-glycoprotein I (aβ2GPI)2. No lupus anticoagulant was detected in any of the patients.


Pre- e post-operative screening in limited-term elective oncological surgery patients during the COVID-19 pandemic period


title: IL‐17A contributes to HSV1 infection‐induced acute lung injury in a mouse model of pulmonary fibrosis

text: BACKGROUND: Patients with idiopathic pulmonary fibrosis (IPF) often experience acute exacerbation (AE) after an episode of common cold. AIMS: To establish a mouse model of virus infection‐induced AE‐IPF and investigate the mechanism underlying the AE‐IPF. METHODS: Herpes simplex virus 1 (HSV1) was inoculated intranasally to wild‐type (WT) and IL‐17A gene knockout (IL‐17A(‐/‐)) mice 21 days after intratracheal administration of bleomycin (BLM). RESULTS: HSV1 infection caused acute exacerbation in mice with BLM‐induced fibrosis. Compared with the BLM+Saline mice, the mice with BLM+HSV1 showed significantly higher acute lung injury (ALI) score (P < 0.0001), lower survival rate (100% vs 21.4%, P < 0.0001), poorer lung function and higher inflammatory response representing by increased total inflammatory cells in bronchoalveolar lavage fluid (BALF) (P = 0.0323), increased proportion of Th17 cells in peripheral blood (P = 0.0004) and higher inflammatory factors in BALF. In addition, HSV1 infection increased the expression of endoplasmic reticulum stress (ERS)‐related proteins in mice with BLM‐induced fibrosis. The inhibition of ERS by tauroursodeoxycholic acid (TUDCA, an ERS inhibitor) significantly reduced the IL‐17A levels in BALF (P = 0.0140) and TH17 cells in the peripheral blood (P = 0.0084) of mice with BLM+HSV1, suggesting that suppression of ERS may reduce TH17 response in mice with AE‐IPF. Compared with WT mice with BLM+HSV1, IL‐17A(‐/‐) mice with BLM+HSV1 had lower ALI score (P = 0.0119), higher survival rate (78.6% vs 21.4%, P = 0.004), improved lung function, and milder inflammatory response. CONCLUSIONS: HSV1 infection in addition to BLM‐induced IPF can successfully establish AE‐IPF in mice. IL‐17A and ERS promote lung inflammation in AE‐IPF development.


title: Performance of a multiplex PCR pneumonia panel for the identification of respiratory pathogens and the main determinants of resistance from the lower respiratory tract specimens of adult patients in intensive care units

text: Abstract Background Timely diagnostic investigation to establish the microbial etiology of pneumonia is essential to ensure the administration of effective antibiotic therapy to individual patients. Methods We evaluated a multiplex PCR assay panel, the FilmArray® pneumonia panel (FilmArray PP, BioFire Diagnostics), for detection of 35 respiratory pathogens and resistance determinants and compared the performance of the standard-of-care test in intensive care unit patients with lower respiratory tract infections. Results Among the 59 endotracheal aspirates and bronchoalveolar lavage specimens obtained from 51 adult patients, FilmArray PP was effective in detecting respiratory bacterial pathogens with an overall positive percent agreement of 90% (95% confidence interval [CI], 73.5–97.9%) and negative percent agreement of 97.4% (95% CI, 96.0–98.4%). FilmArray PP semi-quantitative reporting demonstrated a concordance rate of 53.6% for the culture-positive specimens and 86.3% for the culture-negative specimens. FilmArray PP detected 16 viral targets, whereas the conventional viral isolation failed, except influenza A, which showed 100% concordance with PCR. Coinfections were detected in 42.3% of the specimens. Substantial discrepancies were observed in identifying antimicrobial resistance gene targets and in the susceptibility testing. However, FilmArray PP may still be useful at the early stage of pneumonia before culture and susceptibility test reports are available. Consequently, the results of FilmArray PP might alter the antibiotic prescription in 40.7% of the patients. Conclusions FilmArray PP offers a rapid and sensitive diagnostic method for lower respiratory tract infections. However, clinical correlation is advised to determine its significance in interpreting multiple pathogens and detection of genes involved in antimicrobial resistance.


title: Ionic liquid based ultrasonic assisted extraction of isoflavones from Iris tectorum Maxim and subsequently separation and purification by high-speed counter-current chromatography

text: Abstract We developed an ionic liquid based ultrasonic assisted extraction (ILUAE) method for the extraction of the three isoflavones, namely tectoridin, iristectorin B and iristectorin A from Iris tectorum Maxim of the Iridaceae family. Three kinds of 1-alkyl-3-methylimidazolium ionic liquids with different alkyl chain and anion were investigated. The results indicated that ionic liquids (ILs) showed remarkable effects on the extraction yield of isoflavones. In addition, the ILUAE, including several ultrasonic parameters, such as the concentration, extraction time and solvent to solid ratio have been optimized. Under these optimal conditions (e.g., with 30min extraction time and the solvent to solid ratio of 30ml/g), this approach gained the highest extraction yields of tectoridin (37.45mg/g), iristectorin B (2.88mg/g) and iristectorin A (5.28mg/g). Meanwhile, tectoridin, iristectorin B and iristectorin A in the ILUAE extract were separated and purified successfully through the high-speed counter-current chromatography (HSCCC) with a two-phase solvent system consisting of n-butanol–water (1:1, v/v). The additional advantage of this approach is that 60.21mg tectoridin, 4.33mg iristectorin B and 8.24mg iristectorin A with more than 95.0% purities have been obtained from 400mg ILUAE extract of I. tectorum within 5h and one-step elution under the most optimized conditions (e.g., a flow rate of 2.0ml/min, 900rpm and the wavelengh of 280nm). The obtained fractions were successfully analyzed by HPLC and identified by 1H-NMR and 13C-NMR.


title: Molecular mechanisms regulating CD13-mediated adhesion

text: CD13/Aminopeptidase N is a transmembrane metalloproteinase that is expressed in many tissues where it regulates various cellular functions. In inflammation, CD13 is expressed on myeloid cells, is up-regulated on endothelial cells at sites of inflammation and mediates monocyte/endothelial adhesion by homotypic interactions. In animal models the lack of CD13 alters the profiles of infiltrating inflammatory cells at sites of ischaemic injury. Here, we found that CD13 expression is enriched specifically on the pro-inflammatory subset of monocytes, suggesting that CD13 may regulate trafficking and function of specific subsets of immune cells. To further dissect the mechanisms regulating CD13-dependent trafficking we used the murine model of thioglycollate-induced sterile peritonitis. Peritoneal monocytes, macrophages and dendritic cells were significantly decreased in inflammatory exudates from global CD13(KO) animals when compared with wild-type controls. Furthermore, adoptive transfer of wild-type and CD13(KO) primary myeloid cells, or wild-type myeloid cells pre-treated with CD13-blocking antibodies into thioglycollate-challenged wild-type recipients demonstrated fewer CD13(KO) or treated cells in the lavage, suggesting that CD13 expression confers a competitive advantage in trafficking. Similarly, both wild-type and CD13(KO) cells were reduced in infiltrates in CD13(KO) recipients, confirming that both monocytic and endothelial CD13 contribute to trafficking. Finally, murine monocyte cell lines expressing mouse/human chimeric CD13 molecules demonstrated that the C-terminal domain of the protein mediates CD13 adhesion. Therefore, this work verifies that the altered inflammatory trafficking in CD13(KO) mice is the result of aberrant myeloid cell subset trafficking and further defines the molecular mechanisms underlying this regulation.


title: Quasispecies composition and phylogenetic analysis of feline coronaviruses (FCoVs) in naturally infected cats

text: Quasispecies composition and tissue distribution of feline coronaviruses (FCoVs) were studied in naturally infected cats. The genomic complexity of FCoVs was investigated using single-strand conformational polymorphism (SSCP) analysis of N and ORF7b amplicons, and the evolutionary process was investigated by sequence-based phylogenetic analysis. SSCP analysis showed high heterogeneity of the FCoV genome which was correlated with the seriousness of the clinical form. The two genomic regions analysed showed different levels of variation; the N region demonstrated significant heterogeneity as compared to ORF7b. Phylogenetic analysis of the nucleotide sequences showed the clear separation of sequences analysed on the basis of virulence and geographical origin. A maximum likelihood analysis of N and ORF7b data sets showed a situation of strong heterogeneity for the N region.


title: Performing an urgent neonatal cardiac intervention safely during the COVID-19 pandemic

text: Abstract The current pandemic has driven the medical community to adapt quickly to unprecedented challenges. Among these challenges is the need to minimize staff exposure to COVID-19 during neonatal cardiac procedures. In this report, we describe measures we have taken to protect health care workers while ensuring successful outcomes. These measures include wearing appropriate personal protective equipment, physical distancing, designating separate delivery and transport teams, and limiting the number of providers in direct contact with any patient who is infected or whose infection status is unknown. Learning objectives 1. To understand specific challenges caused by the COVID-19 pandemic 2. To recognize measures that can be taken to minimize health care workers' exposures to the virus during high-risk neonatal cardiac procedures 3. To review the management of neonates with d-transposition of the great arteries and inadequate mixing


title: Overview of Telemedicine and Sleep Disorders

text: Telemedicine is about more than simply using audio-visual technology to care for patients, but rather an opportunity to fundamentally improve patient access, quality, efficiencies, and experience. Regarding sleep medicine, it has the potential to drive sleep medicine’s evolution. By enabling care across geographies and facilitating population-based management, sleep medicine is poised to take advantage of telemedicine capabilities. In this introductory chapter, we highlight issues related to sleep telemedicine, while providing a framework in which to approach this transformational journey thoughtfully. We thereby set the stage for the individual chapters in this edition of Sleep Medicine Clinics.


title: Systems biology of virus entry in mammalian cells

text: In this article, we define systems biology of virus entry in mammalian cells as the discipline that combines several approaches to comprehensively understand the collective physical behaviour of virus entry routes, and to understand the coordinated operation of the functional modules and molecular machineries that lead to this physical behaviour. Clearly, these are extremely ambitious aims, but recent developments in different life science disciplines slowly allow us to set them as realistic, although very distant, goals. Besides classical approaches to obtain high‐resolution information of the molecules, particles and machines involved, we require approaches that can monitor collective behaviour of many molecules, particles and machines simultaneously, in order to reveal design principles of the systems as a whole. Here we will discuss approaches that fall in the latter category, namely time‐lapse imaging and single‐particle tracking (SPT) combined with computational analysis and modelling, and genome‐wide RNA interference approaches to reveal the host components required for virus entry. These techniques should in the future allow us to assign host genes to the systems’ functions and characteristics, and allow emergence‐driven, in silico assembly of networks that include interactions with increasing hierarchy (molecules–multiprotein complexes–vesicles and organelles), and kinetics and subcellular spatiality, in order to allow realistic simulations of virus entry in real time.


title: Differentiation of acid-ph-dependent and -nondependent entry pathways for mouse hepatitis virus

text: Abstract Early events of infection of MHV were studied in comparison with those of VSV, which is known to enter cells by an endocytic pathway. Treatment of mouse L-2 fibroblasts with ammonium chloride, chloroquine, or dansylcadaverine inhibited infection of MHV to a much lesser degree than that of VSV, suggesting a relatively minor role for the endocytic pathway and functional endosomes in MHV infection. Endocytosis of MHV and VSV into L-2 cells was assayed by the recovery of infectious (i.e., not uncoated) viruses from homogenates of cells harvested within the first few minutes of infection (and treated with protease to remove surface-bound virus). The results thus suggest that while a small proportion of the MHV inoculum is internalized by endocytosis, productive infection does not depend on functional endocytosis as utilized by VSV. Studies on direct virion-mediated cell fusion showed that MHV can induce fusion at pH 7.4, whereas VSV causes fusion at pH 5.0. Taken together, the above results suggest that MHV enters L-2 cells predominantly by membrane fusion with a non-acidified compartment such as the plasma membrane, endocytic vesicles, or endosomes (prior to their acidification). Results obtained from cell lines which differed in permissiveness to MHV infection suggested that the ability to support MHV infection does not correlate with endocytosis. Rather, nonpermissive cells, such as rat astrocytoma (C-6) and Vero cells, showed higher levels of recoverable internalized MHV than did fully permissive L-2 cells. Cells which are normally nonpermissive to MHV, could be rendered MHV-susceptible by PEG-induced fusion of cell surface-bound virus. Such PEG-mediated susceptibility to MHV infection was insensitive to inhibition by ammonium chloride, supporting the idea that host cell restriction of MHV infection in C-6 and Vero cells may be due to a block in nonendosomal membrane fusion. Thus endocytic internalization of MHV, which clearly occurs in a variety of cells, does not guarantee productive infection.


La semFYC y la Medicina de Familia en tiempos del Coronavirus


title: Sex and Gender Differences in Health: What the COVID-19 Pandemic Can Teach Us

text: The authors of this commentary call for sex- and gender-specific and differentiating factors to be urgently included in the research, prevention, and therapeutics implementation response to the coronavirus disease 2019 pandemic.


title: Respiratory syncytial virus (RSV) entry is inhibited by serine protease inhibitor AEBSF when present during an early stage of infection

text: BACKGROUND: Host proteases have been shown to play important roles in many viral activities such as entry, uncoating, viral protein production and disease induction. Therefore, these cellular proteases are putative targets for the development of antivirals that inhibit their activity. Host proteases have been described to play essential roles in Ebola, HCV, HIV and influenza, such that specific protease inhibitors are able to reduce infection. RSV utilizes a host protease in its replication cycle but its potential as antiviral target is unknown. Therefore, we evaluated the effect of protease inhibitors on RSV infection. METHODS: To measure the sensitivity of RSV infection to protease inhibitors, cells were infected with RSV and incubated for 18 h in the presence or absence of the inhibitors. Cells were fixed, stained and studied using fluorescence microscopy. RESULTS: Several protease inhibitors, representing different classes of proteases (AEBSF, Pepstatin A, E-64, TPCK, PMSF and aprotinin), were tested for inhibitory effects on an RSV A2 infection of HEp-2 cells. Different treatment durations, ranging from 1 h prior to inoculation and continuing for 18 h during the assay, were evaluated. Of all the inhibitors tested, AEBSF and TPCK significantly decreased RSV infection. To ascertain that the observed effect of AEBSF was not a specific feature related to HEp-2 cells, A549 and BEAS-2B cells were also used. Similar to HEp-2, an almost complete block in the number of RSV infected cells after 18 h of incubation was observed and the effect was dose-dependent. To gain insight into the mechanism of this inhibition, AEBSF treatment was applied during different phases of an infection cycle (pre-, peri- and post-inoculation treatment). The results from these experiments indicate that AEBSF is mainly active during the early entry phase of RSV. The inhibitory effect was also observed with other RSV isolates A1998/3–2 and A2000/3–4, suggesting that this is a general feature of RSV. CONCLUSION: RSV infection can be inhibited by broad serine protease inhibitors, AEBSF and TPCK. We confirmed that AEBSF inhibition is independent of the cell line used or RSV strain. The time point at which treatment with the inhibitor was most potent, was found to coincide with the expected moment of entry of the virion with the host cell.


title: Do we need an ethical framework for hospital infection control?

text: Summary Strategies for the control of the spread of infection in hospitals may lead to constraints on individual autonomy, freedom of movement, or contact with others. Codes of (ethical) practice for healthcare professionals tend to emphasise responsibilities to individual patients. Ethical frameworks for public health focus on groups of individuals (populations), the majority of whom are relatively healthy and empowered. Hospital infection control professionals must take account of both of these perspectives, sensitive to the care of infected and potentially infectious individuals, while protecting the vulnerable and relatively dependent population of hospital patients from further compromise to their health. A number of frameworks for an ethics of public health have been proposed over the last few years but there are sufficient differences in ethical considerations between collective interventions that aim to protect and promote the health of the public and interventions taken in the context of hospital infection control to justify a distinctive ethics of hospital infection control. Professional bodies may be best placed to lead the development of such a framework.


title: Structural analysis of herpes simplex virus by optical super-resolution imaging

text: Herpes simplex virus type-1 (HSV-1) is one of the most widespread pathogens among humans. Although the structure of HSV-1 has been extensively investigated, the precise organization of tegument and envelope proteins remains elusive. Here we use super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM) in combination with a model-based analysis of single-molecule localization data, to determine the position of protein layers within virus particles. We resolve different protein layers within individual HSV-1 particles using multi-colour dSTORM imaging and discriminate envelope-anchored glycoproteins from tegument proteins, both in purified virions and in virions present in infected cells. Precise characterization of HSV-1 structure was achieved by particle averaging of purified viruses and model-based analysis of the radial distribution of the tegument proteins VP16, VP1/2 and pUL37, and envelope protein gD. From this data, we propose a model of the protein organization inside the tegument.


title: Novel highly divergent reassortant bat rotaviruses in Cameroon, without evidence of zoonosis

text: Bats are an important reservoir for zoonotic viruses. To date, only three RVA strains have been reported in bats in Kenya and China. In the current study we investigated the genetic diversity of RVAs in fecal samples from 87 straw-colored fruit bats living in close contact with humans in Cameroon using viral metagenomics. Five (near) complete RVA genomes were obtained. A single RVA strain showed a partial relationship with the Kenyan bat RVA strain, whereas the other strains were completely novel. Only the VP7 and VP4 genes showed significant variability, indicating the occurrence of frequent reassortment events. Comparing these bat RVA strains with currently used human RVA screening primers indicated that most of the novel VP7 and VP4 segments would not be detected in routine epidemiological screening studies. Therefore, novel consensus screening primers were developed and used to screen samples from infants with gastroenteritis living in close proximity with the studied bat population. Although RVA infections were identified in 36% of the infants, there was no evidence of zoonosis. This study identified multiple novel bat RVA strains, but further epidemiological studies in humans will have to assess if these viruses have the potential to cause gastroenteritis in humans.


title: Genomic and antigenic characterization of porcine epidemic diarrhoea virus strains isolated from South Korea, 2017

text: Porcine epidemic diarrhoea virus (PEDV) is a globally emerging and re‐emerging enteric coronavirus in pigs causing serious economic threats to the world swine industry. Since the re‐emergence of massive PEDV outbreaks in South Korea in 2013−2014, domestic pig farms have continued to experience PED epidemics or endemics. This study represents the molecular characterization of PEDV isolates identified in diarrhoeic animals collected across the country in 2017. Initial sequencing analysis of the full‐length S genes revealed that 70% of the 2017 isolates (7/10) belong to the G2b subgroup, while the remaining isolates were classified as G1b. The data indicated that both variant G1b and global epidemic G2b strains were responsible for current PED outbreaks in South Korea. The 2017 G1b and G2b isolates shared 98.7%–99.4% and 98.1%–99.2% amino acid sequence identity at the S gene level and 99.3% and 99.0%–99.6% nucleotide sequence homology at the genome level compared to the corresponding Korean prototype G1b and G2b strains, respectively. In an interesting manner, one G2b‐like KNU‐1705 strain was found to possess a large 39‐nucleotide deletion in the ORF1a region theoretically encoding nonstructural protein 3. Phylogenetic analysis based on the entire genome and spike protein sequences indicated that the 2017 isolates were most closely related to other global G1b or G2b strains but formed different branches within the same genogroup. These results indicate that PEDVs undergo continuous evolution in the field. In addition, one 2017 PEDV strain, KOR/KNU‐1705/2017, was successfully isolated and propagated in Vero cells. The antisera raised against the Korean prototype 2014 G2b strain efficiently neutralized KNU‐1705 virus infection, suggesting antigenic homology between the 2014 and 2017 PEDV strains. Our data advance the understanding of the molecular epidemiology and antigenicity of PEDV circulating in South Korea.


title: Tachycardie atriale chaotique au cours d’une infection respiratoire à coronavirus NL63

text: Résumé Nous rapportons le cas d’un nourrisson de 3 mois hospitalisé pour une bronchiolite. Les troubles respiratoires s’étaient aggravés en 48heures et compliqués d’un état de choc. L’association d’une tachycardie, d’une cardiomégalie et d’une acidose à prédominance métabolique évoquait en premier lieu un choc cardiogénique. L’échocardiographie montrait une défaillance ventriculaire gauche sévère et l’électrocardiogramme mettait en évidence une tachycardie atriale rapide et irrégulière d’aspect chaotique. La recherche étiologique identifiait un coronavirus NL63 dans les aspirations naso-pharyngées, pouvant être à l’origine du trouble du rythme ou d’une atteinte myocardique. L’évolution était favorable en une dizaine de jours après une prise en charge en unité de réanimation comprenant un traitement diurétique (furosémide), anti-arythmique (amiodarone et digoxine) et inotrope (association milrinone–lévosimendan), associé à une ventilation mécanique. Le rythme et la fonction cardiaques s’étaient normalisés à la sortie d’hospitalisation. Summary We report the case of a 3-month-old boy hospitalized with acute bronchiolitis. Respiratory distress was associated with cardiogenic shock caused by chaotic atrial tachycardia. The cause of bronchiolitis was a coronavirus NL63 viral infection, confirmed in nasopharyngeal aspirations. The patient required intensive care including diuretics (furosemide), anti-arrhythmic drugs (amiodarone and digoxin), and inotropic drugs (milrinone and levosimendan) associated with mechanical ventilation. The outcome was favorable in 10days and the sinusal cardiac rhythm was completely restored at discharge.


title: “Watch Out! Pneumonia Secondary to Achromobacter Denitrificans”

text: Pneumonia is the cause of significant morbidity and mortality especially in developing countries. The frequency and importance of emerging new pathogens have significant implications for therapy. We report a case of pneumonia caused by a very rare organism, Achromobacter denitrificans which was treated successfully with intravenous meropenem injections for 14 days. Review of available literature has documentation of isolation of Achromobacter xylosoxidans from endotracheal aspirate culture but this is probably the first case of pneumonia due to A. denitrificans.


title: The dynamic effects of infectious disease outbreaks: The case of pandemic influenza and human coronavirus

text: Pandemic influenza is a regularly recurring form of infectious disease; this work analyses its economic effects. Like many other infectious diseases influenza pandemics are usually of short, sharp duration. Human coronavirus is a less regularly recurring infectious disease. The human coronavirus pandemic of 2019 (COVID-19) has presented with seemingly high transmissibility and led to extraordinary socioeconomic disruption due to severe preventative measures by governments. To understand and compare these events, epidemiological and economic models are linked to capture the transmission of a pandemic from regional populations to regional economies and then across regional economies. In contrast to past pandemics, COVID-19 is likely to be of longer duration and more severe in its economic effects given the greater uncertainty surrounding its nature. The analysis indicates how economies are likely to be affected due to the risk-modifying behaviour in the form of preventative measures taken in response to the latest novel pandemic virus.


title: The first imported case of Rift Valley fever in China reveals a genetic reassortment of different viral lineages

text: We report the first imported case of Rift Valley fever (RVF) in China. The patient returned from Angola, a non-epidemic country, with an infection of a new reassortant from different lineages of Rift Valley fever viruses (RVFVs). The patient developed multiorgan dysfunction and gradually recovered with continuous renal replacement therapy and a short regimen of methylprednisolone treatment. The disordered cytokines and chemokines in the plasma of the patient revealed hypercytokinemia, but the levels of protective cytokines were low upon admission and fluctuated as the disease improved. Whole-genome sequencing and phylogenetic analysis revealed that the imported strain was a reassortant comprising the L and M genes from lineage E and the S gene from lineage A. This case highlights that RVFV had undergone genetic reassortment, which could potentially alter its biological properties, cause large outbreaks and pose a serious threat to global public health as well as the livestock breeding industry.


title: Chapter 6 Natural Products as Cathepsin Inhibitors

text: Abstract Cathepsins are proteases found in all animals as well as other organisms. There are approximately a dozen members of this family, which are distinguished by their structure, their catalytic mechanism, and which proteins they cleave. Most of the members become activated at the low pH found in lysosomes. Cathepsins have been identified as therapeutic targets in the search for new drugs against a number of human pathologies, including cancer, Alzheimer's, and osteoporosis. A number of natural products have been reported as selective inhibitors of some cathepsins. Chemical structure of natural products as inhibitors of cathepsins can be very diverse. Some peptidic natural products are inhibitors of the cysteine protease cathepsins such as E-64 isolated from Aspergillus, which is a cathepsin B inhibitor, or more recently the marine cyanobacterial metabolite gallinamide A which is a selective inhibitor of human cathepsin L. Also amino acid derivatives have been reported as inhibitors of cathepsin A. Other natural products include chalcone natural products possessing cytotoxic activities against prostate cancer cells and inhibiting cysteine cathepsins in vitro, antipain and its analogues isolated from Streptomyces as inhibitors of cathepsin K, and natural biflavones as novel inhibitors of cathepsins B and K. In this review we will report the most representative examples of natural products as inhibitors of cathepsins, especially the ones reported during the last decade.


title: Haematological Cancers and the risk of severe COVID‐19: Exploration and critical evaluation of the evidence to date

text: From the outset of the COVID‐19 pandemic, patients and health care professionals have been concerned that a history of haematological malignancy will lead to an increased risk of severe COVID‐19. This led to the UK government advising patients with blood cancers to shield, massive re‐organisation of NHS haematology and cancer services, and changes in treatment plans for thousands of patients. Given the unknown effects that relaxation of social distancing measures will have on the infection rate, we review the evidence to date to see whether a history of haematological malignancy is associated with increased risk of COVID‐19. Multivariable analysis of large population studies, taking other known risk factors into account do indicate that patients with haematological malignancy, especially those diagnosed recently are at increased risk of death with COVID‐19 compared to the general population. The evidence that this risk is higher than for those with solid malignancies is conflicting. There is suggestive evidence from smaller cohort studies that those with myeloid malignancy may be at increased risk within the blood cancer population, but this needs to be confirmed on larger studies. Ongoing large collaborative efforts are required to gain further evidence regarding specific risk factors for severe complications of COVID‐19.


INSUFICIENCIA RESPIRATORIA COVID-19: SOPORTE CON ECMO PARA NIÑOS Y ADULTOS JÓVENES


title: Low Utility of Repeat Real-Time PCR Testing for SARS-CoV-2 in Clinical Specimens

text: Abstract: In a multicenter cohort of 22,315 patients tested for COVID-19, 1676 (7.5%) had repeat testing via real-time PCR following an initial negative test. Of those retested within seven days of their first negative test, only 2.0% had a positive result. This suggests that repeat testing from the same source is unlikely to provide additional information.


title: Artificial intelligence approach fighting COVID-19 with repurposing drugs

text: BACKGROUND: The ongoing COVID-19 pandemic has caused more than 193,825 deaths during the past few months. A quick-to-be-identified cure for the disease will be a therapeutic medicine that has prior use experiences in patients in order to resolve the current pandemic situation before it could become worsening. Artificial intelligence (AI) technology is hereby applied to identify the marketed drugs with potential for treating COVID-19. MATERIAL AND METHODS: An AI platform was established to identify potential old drugs with anti-coronavirus activities by using two different learning databases; one consisted of the compounds reported or proven active against SARS-CoV, SARS-CoV-2, human immunodeficiency virus, influenza virus, and the other one containing the known 3C-like protease inhibitors. All AI predicted drugs were then tested for activities against a feline coronavirus in in vitro cell-based assay. These assay results were feedbacks to the AI system for relearning and thus to generate a modified AI model to search for old drugs again. RESULTS: After a few runs of AI learning and prediction processes, the AI system identified 80 marketed drugs with potential. Among them, 8 drugs (bedaquiline, brequinar, celecoxib, clofazimine, conivaptan, gemcitabine, tolcapone, and vismodegib) showed in vitro activities against the proliferation of a feline infectious peritonitis (FIP) virus in Fcwf-4 cells. In addition, 5 other drugs (boceprevir, chloroquine, homoharringtonine, tilorone, and salinomycin) were also found active during the exercises of AI approaches. CONCLUSION: Having taken advantages of AI, we identified old drugs with activities against FIP coronavirus. Further studies are underway to demonstrate their activities against SARS-CoV-2 in vitro and in vivo at clinically achievable concentrations and doses. With prior use experiences in patients, these old drugs if proven active against SARS-CoV-2 can readily be applied for fighting COVID-19 pandemic.


title: Inhibition of translation by IFIT family members is determined by their ability to interact selectively with the 5′-terminal regions of cap0-, cap1- and 5′ppp- mRNAs

text: Ribosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA’s 5′-terminal ‘cap’. The minimal ‘cap0’ consists of N7-methylguanosine linked to the first nucleotide via a 5′-5′ triphosphate (ppp) bridge. Cap0 is further modified by 2′-O-methylation of the next two riboses, yielding ‘cap1’ (m7GpppNmN) and ‘cap2’ (m7GpppNmNm). However, some viral RNAs lack 2′-O-methylation, whereas others contain only ppp- at their 5′-end. Interferon-induced proteins with tetratricopeptide repeats (IFITs) are highly expressed effectors of innate immunity that inhibit viral replication by incompletely understood mechanisms. Here, we investigated the ability of IFIT family members to interact with cap1-, cap0- and 5′ppp- mRNAs and inhibit their translation. IFIT1 and IFIT1B showed very high affinity to cap-proximal regions of cap0-mRNAs (K(1/2,app) ∼9 to 23 nM). The 2′-O-methylation abrogated IFIT1/mRNA interaction, whereas IFIT1B retained the ability to bind cap1-mRNA, albeit with reduced affinity (K(1/2,app) ∼450 nM). The 5′-terminal regions of 5′ppp-mRNAs were recognized by IFIT5 (K(1/2,app) ∼400 nM). The activity of individual IFITs in inhibiting initiation on a specific mRNA was determined by their ability to interact with its 5′-terminal region: IFIT1 and IFIT1B efficiently outcompeted eIF4F and abrogated initiation on cap0-mRNAs, whereas inhibition on cap1- and 5′ppp- mRNAs by IFIT1B and IFIT5 was weaker and required higher protein concentrations.


title: A real-time convective PCR machine in a capillary tube instrumented with a CCD-based fluorometer

text: Abstract This research reports the design, analysis, integration, and test of a prototype of a real-time convective polymerase chain reaction (RT-cPCR) machine that uses a color charged coupled device (CCD) for detecting the emission of fluorescence intensity from an RT-cPCR mix in a microliter volume glass capillary. Because of its simple mechanism, DNA amplification involves employing the cPCR technique with no need for thermocycling control. The flow pattern and temperature distribution can greatly affect the cPCR process in the capillary tube, a computational fluid dynamics (CFD) simulation was conducted in this study for the first time to estimate the required period of an RT-cPCR cycle. This study also tested the PCR mix containing hepatitis B virus (HBV) plasmid samples by using SYBR Green I fluorescence labeling dye to assess the prototype performance. The measured results from the image-processing scheme indicate that the RT-cPCR prototype with a CCD-based fluorometer can achieve similar DNA quantification reproducibility compared to commercial machines, even when the initial DNA concentration in the test PCR mix is reduced to 10copies/μL


title: Oseltamivir-Resistant Influenza Viruses A (H1N1) during 2007–2009 Influenza Seasons, Japan

text: To monitor oseltamivir-resistant influenza viruses A (H1N1) (ORVs) with H275Y in neuraminidase (NA) in Japan during 2 influenza seasons, we analyzed 3,216 clinical samples by NA sequencing and/or NA inhibition assay. The total frequency of ORVs was 2.6% (45/1,734) during the 2007–08 season and 99.7% (1,477/1,482) during the 2008–09 season, indicating a marked increase in ORVs in Japan during 1 influenza season. The NA gene of ORVs in the 2007–08 season fell into 2 distinct lineages by D354G substitution, whereas that of ORVs in the 2008–09 season fell into 1 lineage. NA inhibition assay and M2 sequencing showed that almost all the ORVs were sensitive to zanamivir and amantadine. The hemagglutination inhibition test showed that ORVs were antigenetically similar to the 2008–09 vaccine strain A/Brisbane/59/2007. Our data indicate that the current vaccine or zanamivir and amantadine are effective against recent ORVs, but continuous surveillance remains necessary.


title: scRNA-seq Profiling of Human Testes Reveals the Presence of the ACE2 Receptor, A Target for SARS-CoV-2 Infection in Spermatogonia, Leydig and Sertoli Cells

text: In December 2019, a novel coronavirus (SARS-CoV-2) was identified in COVID-19 patients in Wuhan, Hubei Province, China. SARS-CoV-2 shares both high sequence similarity and the use of the same cell entry receptor, angiotensin-converting enzyme 2 (ACE2), with severe acute respiratory syndrome coronavirus (SARS-CoV). Several studies have provided bioinformatic evidence of potential routes of SARS-CoV-2 infection in respiratory, cardiovascular, digestive and urinary systems. However, whether the reproductive system is a potential target of SARS-CoV-2 infection has not yet been determined. Here, we investigate the expression pattern of ACE2 in adult human testes at the level of single-cell transcriptomes. The results indicate that ACE2 is predominantly enriched in spermatogonia and Leydig and Sertoli cells. Gene Set Enrichment Analysis (GSEA) indicates that Gene Ontology (GO) categories associated with viral reproduction and transmission are highly enriched in ACE2-positive spermatogonia, while male gamete generation related terms are downregulated. Cell–cell junction and immunity-related GO terms are increased in ACE2-positive Leydig and Sertoli cells, but mitochondria and reproduction-related GO terms are decreased. These findings provide evidence that the human testis is a potential target of SARS-CoV-2 infection, which may have significant impact on our understanding of the pathophysiology of this rapidly spreading disease.


title: Lineages, Sub-Lineages and Variants of Enterovirus 68 in Recent Outbreaks

text: Enterovirus 68 (EV68) was first isolated in 1962. Very few cases of EV68 infection were described over the ensuing 40 years. However, in the past few years, an increase in severe respiratory tract infections associated with EV68 has been reported. We identified two clusters of EV68 infection in South London, UK, one each in the autumn/winters of 2009 and 2010. Sequence comparison showed significant homology of the UK strains with those from other countries including the Netherlands, Japan and the Philippines, which reported EV68 outbreaks between 2008 and 2010. Phylogenetic analysis of all available VP1 sequences indicated the presence of two modern EV68 lineages. The 2010 UK strains belonged to lineage 2. Lineage 1 could be further divided into two sub-lineages: some Japanese and Dutch strains collected between 2004 and 2010 form a distinct sub-lineages (sub-lineage 1.1), whereas other strains from the UK, Japan, Netherlands and Philippines collected between 2008 and 2010 represent sub-lineage 1.2. The UK 2009 strains together with several Dutch and Japanese strains from 2009/2010 represents one variant (1.2.1), whereas those from the Philippines a second variant (1.2.2). Based on specific deletions and substitutions, we suggest rules for the assignment of lineages and sub-lineages. Molecular epidemiological analysis indicates rapid recent evolution of EV68 and this may explain the recent findings of a global resurgence of EV68. Continuous global monitoring of the clinical and molecular epidemiology of EV68 is recommended.


title: Chapter 4 Gene–Environment Interactions Eco-Genetics and Toxicogenomics

text: Gene–environment interactions likely account for a large portion of the “missing heritability” or “dark matter” of genetic associations with traits and diseases. In concert with the powerful methods and scale of genomic population analyses, a complementary effort is needed to capture data about behavioral and environmental variables acting on the genetic substrate and contributing importantly to disease risk. Examples from environmental exposures to foods and food additives, infectious agents, inhaled pollutants, pesticides, pharmaceuticals, sensory stimuli, and allergic and sensitizing agents are summarized. Epigenomics and protein folding/misfolding are recently recognized mechanisms for some of these interactions and effects. Keywords asthma, cancers, eco-genetics, epigenomics, evolution, gene–environment interactions, genome-wide association studies, heritability, host susceptibility, nutrigenomics, pathogens, toxicogenomics


Adaptation of the ‘Assembly Line’ and ‘Brick System’ techniques for hospital resource management of personal protective equipment, as preparedness for mitigating the impact of the COVID-19 pandemic in a large public hospital in India


Workshop on “The Role of Indoor Air as a Vehicle for Human Pathogens”: A Panel Discussion


title: Effect of Porcine Epidemic Diarrhea Virus Infectious Doses on Infection Outcomes in Naïve Conventional Neonatal and Weaned Pigs

text: Porcine epidemic diarrhea virus (PEDV) was identified in the United States (U.S.) swine population for the first time in April 2013 and rapidly spread nationwide. However, no information has been published regarding the minimum infectious dose (MID) of PEDV in different pig models. The main objective of this study was to determine the oral minimum infectious dose of PEDV in naïve conventional neonatal piglets and weaned pigs. A U.S. virulent PEDV prototype isolate (USA/IN19338/2013) with known infectious titer was serially ten-fold diluted in virus-negative cell culture medium. Dilutions with theoretical infectious titers from 560 to 0.0056 TCID(50)/ml together with a medium control were orogastrically inoculated (10ml/pig) into 7 groups of 5-day-old neonatal pigs (n = 4 per group) and 7 groups of 21-day-old weaned pigs (n = 6 per group). In 5-day-old pigs, 10ml of inoculum having titers 560–0.056 TCID(50)/ml, corresponding to polymerase chain reaction (PCR) cycle threshold (Ct) values 24.2–37.6, resulted in 100% infection in each group; 10ml of inoculum with titer 0.0056 TCID(50)/ml (Ct>45) caused infection in 25% of the inoculated pigs. In 21-day-old pigs, 10ml of inoculum with titers 560–5.6 TCID(50)/ml (Ct 24.2–31.4) resulted in 100% infection in each group while 10ml of inoculum with titers 0.56–0.0056 TCID(50)/ml (Ct values 35.3 –>45) did not establish infection in any pigs under study conditions as determined by clinical signs, PCR, histopathology, immunohistochemistry, and antibody response. These data reveal that PEDV infectious dose is age-dependent with a significantly lower MID for neonatal pigs compared to weaned pigs. This information should be taken into consideration when interpreting clinical relevance of PEDV PCR results and when designing a PEDV bioassay model. The observation of such a low MID in neonates also emphasizes the importance of strict biosecurity and thorough cleaning/disinfection on sow farms.


title: Complete genome sequence analysis of canine bocavirus 1 identified for the first time in domestic cats

text: In this study, we investigated the presence of canine bocaviruses (CBoVs) in fecal samples from 105 cats with diarrhea and 92 asymptomatic cats in northeast China. One fecal sample, 17CC0312, collected from an asymptomatic cat, was found to be positive for canine bocavirus 1 (CBoV1). The nearly complete genome of this virus was cloned and sequenced. The viral genome was 5,069 nucleotides (nt) in length and combined four open reading frames (ORFs) in the order 5′-NS1-ORF4-NP1-VP1/VP2-3′. The 17CC0312 virus shared more than 90.3% nucleotide sequence identity with CBoV1 reference sequences and was placed within the CBoV1 group in a phylogenetic tree based on complete genome sequences. Further phylogenetic analysis based on the deduced amino acid sequence of the VP2 gene showed that this feline CBoV1 strain belongs to CBoV1 lineage 3. These data provide the first molecular evidence of the presence of CBoV1 in a domestic cat and suggest that cats might be carriers of CBoV1.


title: Effet bénéfique de l’association Hydroxychloroquine-Azithromycine dans le traitement des patients âgés atteints de la covid-19: résultats d’une étude observationnelle

text: Summary Sixty-eight patients, all over 65 years of age and diagnosed PCR-positive for covid-19, received the hydroxychloroquine / azithromycin combination between March 27 and May 1, 2020.Dosages of hydroxychloroquine and azithromycin were in accordance with the protocol of the Institut Hospitalo-Universitaire de Marseille. The mean age was 86.4 ± 8.2 years, mean BMI was 22.8 ± 5.2 kg/m2. Nineteen patients were overweight (BMI greater than 25 kg / m2), four of whom were obese (BMI greater than 30 kg / m2). Seven patients had renal impairment of less than 30 mL / min.The survey of associated conditions indicated that about 51.5% of patients had high blood pressure while 28% had heart disease. Of these, 16.2% had diabetes. Only one patient had asthma and one had COPD.Two patients had to stop their treatment after 3 and 9 days of dual therapy respectively due to QTc prolongation. The objective of our study was to evaluate the efficacy of the hydroxychloroquine-azithromycin combination in elderly subjects with covid-19.During the study period, 7 of the 68 patients studied died. All deaths occurred due to severe respiratory complications of the disease. The remaining patients were considered cured after clinical signs disappeared 21 days after the PCR+ test.


title: COVID-19 Outbreak in North Italy: An Overview on Dentistry. A Questionnaire Survey

text: This survey assessed the symptoms/signs, protective measures, awareness, and perception levels regarding COVID-19 among dentists in Lombardy, Italy. Moreover, an analysis of the answers gathered in areas with different prevalence of the disease was carried out. All Lombardy’s dentists were sent an online ad hoc questionnaire. The questionnaire was divided into four domains: personal data, precautionary measures (before patient arrival; in the waiting room; in the operating room), awareness, and perception. Three thousand five hundred ninety-nine questionnaires were analyzed. Five hundred two (14.43%) participants had suffered one or more symptoms referable to COVID-19. Thirty-one subjects were positive to the virus SARS-CoV-2 and 16 subjects developed the disease. Only a small number of dentists (n = 72, 2.00%) were confident of avoiding infection; dentists working in low COVID-19 prevalence areas were more confident than those working in the Milan area and high prevalence area (61.24%, 61.23%, and 64.29%, p < 0.01 respectively). The level of awareness was statistically significantly higher (p < 0.01) in the Milan area (71.82%) than in the other areas. This survey demonstrated that dentists in the COVID-19 highest prevalence area, albeit reported to have more symptoms/signs than the rest of the sample, were the ones who adopted several precautionary measures less frequently and were the more confident of avoiding infection.


title: n-butanol extract from Folium isatidis inhibits the lipopolysaccharide-induced downregulation of CXCR1 and CXCR2 on human neutrophils

text: Neutrophils, immune cells crucial for protecting against invading pathogens, are important in sepsis. Neutrophil migration is regulated by chemokine receptors and their cognate ligands. Our previous study investigated the effect of n-butanol extract from Folium isatidis on lipopolysaccharide (LPS)-induced septic shock. The present study stimulated neutrophils with LPS to explore the influence of LPS on cell. Neutrophils were then pretreated with n-butanol extract from Folium isatidis followed by LPS to examine the effect of this extract on neutrophil chemotaxis. The results showed that LPS decreased the expression levels of CXC-chemokine receptor (CXCR)1, CXCR2 and L-selectin (CD62L), and increased the expression of interleukin-8 (IL-8) by neutrophils. The addition of n-butanol extract from Folium isatidis inhibited this LPS-induced downregulation of CXCR1, CXCR2 and CD62L, and decreased the expression of IL-8 on neutrophils. In addition, n-butanol extract promoted myeloperoxidase activity in neutrophils. Taken together, LPS downregulated the expression of chemokine receptors, leading to the failure of neutrophils to migrate to sites of infection. The addition of n-butanol extract, which promoted the ability of neutrophils to migrate, is a natural product and potential therapeutic agent with which to target neutrophil chemotaxis during LPS stimulation.