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

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


Molecular Interactions of Group 1 Coronaviruses with Feline APN


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

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


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


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

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


Wear N95 Mask With Plastic Handle Reduce Pressure Injury


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

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


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

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


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

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


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

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


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

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


title: lncRNA expression signatures in response to enterovirus 71 infection

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


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

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


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

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


title: Reactivation of SARS‐CoV‐2 after Recovery

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


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

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


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

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


Collapsing glomerulopathy in a COVID-19 patient.


title: Total Chemical Synthesis of ISGylated-Ubiquitin Hybrid Chain Assisted by Acetamidomethyl Derivatives with Dual Functions

text: [Image: see text] Interferon-stimulated gene 15 (ISG15) is a member of the ubiquitin-like modifiers (ULM) family, which adopts a β-grasp fold domain(s) similar to ubiquitin (Ub) with only minor sequence homology. ISG15 consists of two Ub-like domains and aids the immune system in neutralizing infections by numerous pathogens and plays an important role in defending cells against many viruses including influenza A. Recently, Ub was found to be a substrate for ISG15, which can be ISGylated on Lys29 and Lys48, while the former is more dominant. The discovery of such hybrid ISG15-Ub chains brought forward various fundamental questions regarding the nature and effect of this conjugation. To further investigate the role of hybrid ISG15-Ub chains, the pure homogeneous material of these chains is needed in workable quantities. By applying advanced chemical strategies for protein synthesis, we report the total chemical synthesis of a 231-residue ISG15-Lys29-Ub hybrid chain. During the synthesis we encountered insoluble peptide fragments, and therefore we developed a new reversible Acm based solubilizing tag to efficiently tackle this hurdle. This new Acm tag was compared with the known Arg based Acm solubilizing tag and was found to be more reliable in terms of incorporation and efficiency as demonstrated in the synthesis of the native ISG15-Ub hybrid chain.


Infectious Diseases of the Nervous System and Their Impact in Developing Countries


title: Interferon-λ: immune functions at barrier surfaces and beyond

text: When type III interferon (IFN-λ; also known as interleukin-28 (IL-28) and IL-29) was discovered in 2003, its antiviral function was expected to be analogous to the type I IFNs (IFN-α and IFN-β), via the induction of IFN-stimulated genes (ISGs). While IFN-λ stimulates expression of antiviral ISGs preferentially in cells of epithelial origin, recent studies have defined additional antiviral mechanisms in other cell types and tissues. Models of viral infection using mice lacking IFN-λ signaling and single nucleotide polymorphism (SNP) associations with human disease have expanded our understanding of the contribution of IFN-λ to the antiviral response at anatomic barriers and the immune response beyond these barriers. In this review, we highlight recent insights into the functions of IFN-λ, including its ability to restrict virus spread into the brain and to clear chronic viral infections in the gastrointestinal tract. We also discuss how IFN-λ modulates innate and adaptive immunity, autoimmunity, and tumor progression and its possible therapeutic applications in human disease.


title: The Middle East Respiratory Syndrome—How Worried Should We Be?

text: Ten years after the severe acute respiratory syndrome epidemic, a second coronavirus, the Middle East respiratory syndrome coronavirus (MERS-CoV), has been identified as the cause of a highly lethal pneumonia in patients in the Middle East and in travelers from this region. Over the past 9 months, since the virus was first isolated, much has been learned about the biology of the virus. It is now clear that MERS-CoV is transmissible from person to person, and its close relationship with several bat coronaviruses suggests that these animals may be the ultimate source of the infection. However, many key issues need to be addressed, including identification of the proximate, presumably zoonotic, source of the infection, the prevalence of the infection in human populations, details regarding clinical and pathological features of the human infection, the establishment of a small rodent model for the infection, and the virological and immune basis for the severe disease observed in most patients. Most importantly, we do not know whether a MERS-CoV epidemic is likely or not. Infection with the virus has so far resulted in only 91 cases and 46 deaths (as of 29 July 2013), but it is nonetheless setting off alarm bells among public health officials, including Margaret Chan, Director-General of the World Health Organization, who called MERS-CoV “a threat to the entire world.” This article reviews some of the progress that has been made and discusses some of the questions that need to be answered.


title: A Simulation of a COVID-19 Epidemic Based on a Deterministic SEIR Model

text: An epidemic disease caused by a new coronavirus has spread in Northern Italy with a strong contagion rate. We implement an SEIR model to compute the infected population and the number of casualties of this epidemic. The example may ideally regard the situation in the Italian Region of Lombardy, where the epidemic started on February 24, but by no means attempts to perform a rigorous case study in view of the lack of suitable data and the uncertainty of the different parameters, namely, the variation of the degree of home isolation and social distancing as a function of time, the initial number of exposed individuals and infected people, the incubation and infectious periods, and the fatality rate. First, we perform an analysis of the results of the model by varying the parameters and initial conditions (in order for the epidemic to start, there should be at least one exposed or one infectious human). Then, we consider the Lombardy case and calibrate the model with the number of dead individuals to date (May 5, 2020) and constrain the parameters on the basis of values reported in the literature. The peak occurs at day 37 (March 31) approximately, with a reproduction ratio R(0) of 3 initially, 1.36 at day 22, and 0.8 after day 35, indicating different degrees of lockdown. The predicted death toll is approximately 15,600 casualties, with 2.7 million infected individuals at the end of the epidemic. The incubation period providing a better fit to the dead individuals is 4.25 days, and the infectious period is 4 days, with a fatality rate of 0.00144/day [values based on the reported (official) number of casualties]. The infection fatality rate (IFR) is 0.57%, and it is 2.37% if twice the reported number of casualties is assumed. However, these rates depend on the initial number of exposed individuals. If approximately nine times more individuals are exposed, there are three times more infected people at the end of the epidemic and IFR = 0.47%. If we relax these constraints and use a wider range of lower and upper bounds for the incubation and infectious periods, we observe that a higher incubation period (13 vs. 4.25 days) gives the same IFR (0.6 vs. 0.57%), but nine times more exposed individuals in the first case. Other choices of the set of parameters also provide a good fit to the data, but some of the results may not be realistic. Therefore, an accurate determination of the fatality rate and characteristics of the epidemic is subject to knowledge of the precise bounds of the parameters. Besides the specific example, the analysis proposed in this work shows how isolation measures, social distancing, and knowledge of the diffusion conditions help us to understand the dynamics of the epidemic. Hence, it is important to quantify the process to verify the effectiveness of the lockdown.


title: Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode

text: The main protease (M(pro)) plays a vital role in proteolytic processing of the polyproteins in the replicative cycle of SARS coronavirus (SARS-CoV). Dimerization of this enzyme has been shown to be indispensable for transcleavage activity. However, the auto-processing mechanism of M(pro), i.e. its own release from the polyproteins through autocleavage, remains unclear. This study elucidates the relationship between the N-terminal autocleavage activity and the dimerization of “immature” M(pro). Three residues (Arg4, Glu290, and Arg298), which contribute to the active dimer conformation of mature M(pro), are selected for mutational analyses. Surprisingly, all three mutants still perform N-terminal autocleavage, while the dimerization of mature protease and transcleavage activity following auto-processing are completely inhibited by the E290R and R298E mutations and partially so by the R4E mutation. Furthermore, the mature E290R mutant can resume N-terminal autocleavage activity when mixed with the “immature” C145A/E290R double mutant whereas its trans-cleavage activity remains absent. Therefore, the N-terminal auto-processing of M(pro) appears to require only two “immature” monomers approaching one another to form an “intermediate” dimer structure and does not strictly depend on the active dimer conformation existing in mature protease. In conclusion, an auto-release model of M(pro) from the polyproteins is proposed, which will help understand the auto-processing mechanism and the difference between the autocleavage and trans-cleavage proteolytic activities of SARS-CoV M(pro).


title: SARS-CoV-2-specific T cells exhibit unique features characterized by robust helper function, lack of terminal differentiation, and high proliferative potential

text: Convalescing COVID-19 patients mount robust T cell responses against SARS-CoV-2, suggesting an important role for T cells in viral clearance. To date, the phenotypes of SARS-CoV-2-specific T cells remain poorly defined. Using 38-parameter CyTOF, we phenotyped longitudinal specimens of SARS-CoV-2-specific CD4+ and CD8+ T cells from four individuals who recovered from mild COVID-19. SARS-CoV-2-specific CD4+ T cells were exclusively Th1 cells, and predominantly Tcm with phenotypic features of robust helper function. SARS-CoV-2-specific CD8+ T cells were predominantly atypical Temra cells in a state of less terminal differentiation and therefore capable of expansion. Subsets of SARS-CoV-2-specific T cells exhibit features of being long-lived and capable of homeostatic proliferation consistent with their persistence for over two months. Our results suggest that long-lived and robust T cell immunity is generated following natural SARS-CoV-2 infection, and support an important role for SARS-CoV-2-specific T cells in host control of COVID-19.


title: A new recruit for the army of the men of death

text: The army of the men of death, in John Bunyan's memorable phrase, has a new recruit, and fear has a new face: a face wearing a surgical mask.


RNA pseudoknots that interact with components of the translation apparatus


Chapter 2 Standard Precautions


title: Survival in a zombie apocalypse

text: The Resident Evil 3 remake was in development long before the coronavirus outbreak, but it holds up a mirror to the strange times we live in today, says Jacob Aron


title: Monoclonal antibodies for prophylactic and therapeutic use against viral infections

text: Abstract Neutralizing antibodies play an essential part in antiviral immunity and are instrumental in preventing or modulating viral diseases. Polyclonal antibody preparations are increasingly being replaced by highly potent monoclonal antibodies (mAbs). Cocktails of mAbs and bispecific constructs can be used to simultaneously target multiple viral epitopes and to overcome issues of neutralization escape. Advances in antibody engineering have led to a large array of novel mAb formats, while deeper insight into the biology of several viruses and increasing knowledge of their neutralizing epitopes has extended the list of potential targets. In addition, progress in developing inexpensive production platforms will make antiviral mAbs more widely available and affordable.


Non-SARS CoV2 positive critical patients: sons of a lesser God?


title: Tracheostomy protocols during COVID‐19 pandemic

text: BACKGROUND: The COVID‐19 pandemic has resulted in the implementation of rapidly changing protocols and guidelines related to the indications and perioperative precautions and protocols for tracheostomy. The purpose of this study was to evaluate current guidelines for tracheostomy during the COVID‐19 pandemic to provide a framework for health systems to prepare as the science evolves over the upcoming months and years. METHODS: Literature review was performed. Articles reporting clinical practice guidelines for tracheostomy in the context of COVID‐19 were included. RESULTS: A total of 13 tracheotomy guidelines were identified. Two were available via PubMed, five in society or organization websites, and six identified via health system websites or other sources. Five were from Otolaryngology‐Head and Neck Surgery specialties, six from Anesthesiology and one from Pulmonary/Critical Care. All (100%) studies recommended postponing elective OR cases in COVID‐19 positive patients, while seven recommended reducing team members to only essential staff and three recommended forming a designated tracheostomy team. Recommendations with supporting references are summarized in the article. CONCLUSIONS: Tracheostomy guidelines during the COVID‐19 pandemic vary by physician groups and specialty, hospital systems, and supply‐chain/resource availability. This summary is provided as a point‐in‐time current state of the guidelines for tracheotomy management in April 2020 and is expected to change in coming weeks and months as the COVID‐19 pandemic, virus testing and antibody testing evolves.


title: Mortality and the use of Antithrombotic Therapies among Nursing Home Residents with COVID‐19

text: BACKGROUND/OBJECTIVES: Nursing home (NH) residents are a vulnerable population, susceptible to respiratory disease outbreaks such as coronavirus disease 2019 (COVID‐19). Poor outcome in COVID‐19 is at least partly attributed to hypercoagulability, resulting in a high incidence of thromboembolic complications. It is unknown whether commonly used antithrombotic therapies may protect the vulnerable NH population with COVID‐19 against mortality. This study aimed to investigate whether the use of oral antithrombotic therapy (OAT) was associated with a lower mortality in NH residents with COVID‐19. DESIGN: A retrospective case‐series SETTING: 14 NH facilities from the NH organization Envida, Maastricht, the Netherlands PARTICIPANTS: 101 NH residents with COVID‐19 were enrolled. MEASUREMENTS: The primary outcome was all‐cause mortality. The association between age, sex, comorbidity, OAT, and mortality was assessed using logistic regression analysis. RESULTS: Overall mortality was 47.5% in NH residents from 14 NH facilities. Age, comorbidity and medication use were comparable among NH residents who survived and who died. OAT was associated with a lower mortality in NH residents with COVID‐19 in the univariable analysis (OR 0.89 95%CI 0.41‐1.95). However, additional adjustments for sex, age and comorbidity, attenuated this difference. Mortality in males was higher compared with female residents (OR 3.96 (95%CI 1.62‐9.65)). Male residents who died were younger compared to female residents (82.2 (SD 6.3) vs. 89.1 years (SD 6.8), p<.001). CONCLUSION: NH residents in the 14 facilities we studied were severely affected by the COVID‐19 pandemic, with a mortality of 47.5%. Male NH residents with COVID‐19 had worse outcomes than females. We did not find evidence for any protection against mortality by OAT, necessitating further research into strategies to mitigate poor outcome of COVID‐19 in vulnerable NH populations. This article is protected by copyright. All rights reserved.


title: International cooperation during the COVID-19 pandemic

text: This paper explores the concept of ‘global public goods’ (GPGs) in the context of the ongoing COVID-19 pandemic. It argues that many of the tasks involved in public health, and in particular those involved in the control of an infectious disease like COVID-19, ought to be treated as GPGs that can only be effectively delivered through international cooperation. It sets out what a cooperative response to the COVID-19 pandemic should look like and introduces ideas for further discussion about how it might be financed.


COVID-19 in pediatric patients: what the prehospital teams need to know


title: Molecular Insights into Poly(ADP-ribose) Recognition and Processing

text: Poly(ADP-ribosyl)ation is a post-translational protein modification involved in the regulation of important cellular functions including DNA repair, transcription, mitosis and apoptosis. The amount of poly(ADP-ribosyl)ation (PAR) in cells reflects the balance of synthesis, mediated by the PARP protein family, and degradation, which is catalyzed by a glycohydrolase, PARG. Many of the proteins mediating PAR metabolism possess specialised high affinity PAR-binding modules that allow the efficient sensing or processing of the PAR signal. The identification of four such PAR-binding modules and the characterization of a number of proteins utilising these elements during the last decade has provided important insights into how PAR regulates different cellular activities. The macrodomain represents a unique PAR-binding module which is, in some instances, known to possess enzymatic activity on ADP-ribose derivatives (in addition to PAR-binding). The most recently discovered example for this is the PARG protein, and several available PARG structures have provided an understanding into how the PARG macrodomain evolved into a major enzyme that maintains PAR homeostasis in living cells.


title: Domestication and the behavior-genetic analysis of captive populations

text: Abstract Captive environments are believed to produce behavioral changes in animal populations that may limit our ability to generalize back to natural populations. These behavioral changes are thought to be associated with one or both of the following: (a) changes in frequencies of genes or gene complexes due to the effects of inbreeding or to changes in selection pressure; (b) changes in development of the phenotype due to the effects of changes in environmental variables. Inbreeding leads to increase in homozygosity, that may result in developmental anomalies because of a breakdown in developmental homeostasis. Changes in selection pressure may disrupt coadapted gene complexes that have evolved in the wild. Often, domestication is believed to result in individuals that are “degenerate”; i.e. inferior to individuals in the wild. However, this notion has received no empirical support. In fact, if phenotype changes do occur under domestication, these are usually quantitative, not qualitative, in nature. We suggest that the study of the domestication process may reveal evolutionary principles that would be difficult to discover in other ways, and the zoological parks may be ideal situations for such research.


title: Reverse transcription polymerase chain reaction (RT‐PCR) for diagnosis of respiratory syncytial virus infection in adults: Use of a single‐tube “hanging droplet” nested PCR

text: Rapid diagnosis of Respiratory Syncytial virus (RSV) infection is difficult in elderly persons due to the low quantities of virus shed. Therefore, reverse transcription‐polymerase chain reaction (RT‐PCR) was used to detect viral RNA in respiratory secretions. A single‐tube nested RT‐PCR that used primers from a conserved F gene sequence was developed using a “hanging droplet” to physically separate outer and inner primer pairs during the first round of the PCR reaction. This was accomplished by placing the inner primers in a 5 μL droplet on the underside on the reaction tube cap and mixing after the first round of PCR. As few as 0.05 pfu of virus could be detected and gave positive results with RSV strains that represented the major groups and subgroups of RSV grown in tissue culture. The nested PCR was ∼100‐fold more sensitive than standard single primer PCR reactions and equivalent to standard two‐tube nested PCR. Viral RNA was detected in nasopharyngeal samples from 12 of 15 culture positive illnesses and in 5 of 17 culture‐negative, seropositive illnesses despite specimen volumes less than 1 μL in some samples. The method was also positive in 14 of 25 elderly volunteers inoculated with a live attenuated RSV vaccine candidate, only one of whom was culture positive. Use of a nested RT‐PCR significantly improves the ability to detect RSV in respiratory samples and should improve the ability to rapidly diagnose RSV infection in adults, especially in the elderly. J. Med. Virol. 63:259–263, 2001. © 2001 Wiley‐Liss, Inc.


title: Learning from Ebola: Interprofessional practice in the Nebraska Biocontainment Unit

text: Abstract Caring for patients with Ebola virus disease (EVD) in the Nebraska Biocontainment Unit (NBU) has necessitated and enabled extensive interprofessional relationships and the creation of a collaborative care model. Critical aspects of NBU functionality include a constructive leadership environment, staff inclusion and consideration during protocol development, and a culture of partnership and communication.


Position Paper: EUFEPS Network on Veterinary Medicines Initiative


Preserving the “human touch” in times of COVID-19


title: Tackling the Global Challenge: Humanitarian Catastrophes

text: “Humanitarian catastrophes,” conflicts and calamities generating both widespread human suffering and destructive events, require a wide range of emergency resources. This paper answers a number of questions that humanitarian catastrophes generate: Why and how do the most-developed countries—those with the resources, capabilities, and willingness to help—intervene in specific types of disasters? What ethical and legal guidelines shape our interventions? How well do we achieve our goals? It then suggests a number of changes to improve humanitarian responses, including better NGO-government cooperation, increased research on the best disaster response methods, clarification of the criteria and roles for humanitarian (military) interventions, and development of post-2015 Millennium Development Goals with more accurate progress measures.


title: An update on feline infectious peritonitis: Diagnostics and therapeutics

text: Abstract This review is concerned with what has been learned about feline infectious peritonitis (FIP) diagnostics and therapeutics since the publication of an extensive overview of literature covering the period 1963–2009. Although progress has been made in both areas, obtaining a definitive diagnosis of FIP remains a problem for those veterinarians and/or cat owners who require absolute certainty. This review will cover both indirect and direct diagnostic tests for the disease and will emphasize their limitations, as well as their specificity and sensitivity. There is still no effective treatment for FIP, although there are both claims that such therapies exist and glimmers of hope coming from new therapies that are under research. FIP has also been identified in wild felids and FIP-like disease is now a growing problem among pet ferrets.


title: Dynamics of an SEIR model with infectivity in incubation period and homestead-isolation on the susceptible

text: Abstract In this paper, we presents an SEIR epidemic model with infectivity in incubation period and homestead-isolation on the susceptible. We prove that the infection-free equilibrium point is locally and globally asymptotically stable with condition R 0 < 1 . We also prove that the positive equilibrium point is locally and globally asymptotically stable with condition R 0 > 1 . Numerical simulations are employed to illustrate our results. In the absence of vaccines or antiviral drugs for the virus, our results suggest that the governments should strictly implement the isolation system to make every effort to curb propagation of disease during the epidemic.


title: 2 US federal oversight of biological materials and the IBC

text: Abstract This chapter will give a thorough overview of the laws and guidelines regulating research use of biological materials in the United States and how Institutional Biosafety Committees (IBC) came to be tasked with providing oversight for these activities. The anthrax attacks after 9/11 demonstrated that information gained from life science research can be used to threaten national security and public health. Since these attacks, the public has demanded increased oversight of research. IBC oversight falls under the National Institutes of Health Guidelines. Over the years, other federal agencies have increased the demands on the IBC by promulgating new legislation and regulations. The following agencies play a role in regulating research: National Science Advisory Board for Biosecurity, National Research Council, National Institutes of Health, Food and Drug Administration, Environmental Protection Agency, Department of Human and Health Services, U.S. Department of Agriculture, and Department of Justice.


title: Cholesterol Supplementation During Production Increases the Infectivity of Retroviral and Lentiviral Vectors Pseudotyped with the Vesicular Stomatitis Virus Glycoprotein (VSV-G)

text: Cholesterol, a major component of plasma membrane lipid rafts, is important for assembly and budding of enveloped viruses, including influenza and HIV-1. Cholesterol depletion impairs virus assembly and infectivity. This study examined the effects of exogenous cholesterol addition (delivered as a complex with methyl beta cyclodextrin) on the production of Molony murine leukemia virus retroviral vector and HIV-1-based lentiviral vector pseudotyped with the vesicular stomatitis virus glycoprotein (VSV-G). Cholesterol supplementation before and during vector production enhanced the infectivity of retroviral and lentiviral vectors up to 4-fold and 6-fold, respectively. In contrast, the amount of retroviral vector produced was unchanged, and that of lentiviral vector was increased less than two-fold. Both free cholesterol and cholesterol ester content in 293-gag-pol producer cells increased with cholesterol addition. In contrast, the phospholipids headgroup composition was essentially unchanged by cholesterol supplementation in 293-gag-pol packaging cells. Based on these results, it is proposed that cholesterol supplementation increases the infectivity of VSV-G-pseudotyped retroviral and lentiviral vectors, possibly by altering the composition of the producer cell membrane where the viral vectors are assembled and bud, and/or by changing the lipid composition of the viral vectors.


Human metapneumovirus infection in children hospitalized for wheezing


title: Fine-tuning of type I IFN-signaling in microglia — implications for homeostasis, CNS autoimmunity and interferonopathies

text: Type I interferons (IFN) are pleiotropic cytokines originally described as molecules used for communication between cells to trigger the protective defenses against viral infections. Upon activation, type I IFN can be produced locally in the central nervous system (CNS) from a number of different cell types including microglia, the CNS-resident macrophages. Increased type I IFN production and signaling in microglia are critically important to limit viral infection and disease progression in multiple sclerosis. However, recent findings suggest that even baseline levels of constitutive IFN expression and secretion are important for homeostasis of the CNS. In fact, in the absence of viral particles chronic elevation of IFN I may be tremendously harmful for the CNS, as assumed for patients suffering from Aicardi-Goutières syndrome, Cree encephalitis or other type I interferonopathies. The highly diverse nature of type I IFN for brain homeostasis during health and disease will be discussed in this report.


title: The devolution of the social licence to operate in the Australian mining industry

text: The aim of this paper is to present a brief historical analysis of the Australian mining industry and the development of its social licence to operate. Commencing with the discovery of coal in the 18th century, to gold and copper and base metals in the 19th century, to the world class iron ore, mineral sands and diamond mines of the 20th century to the current day, the paper will attempt to determine how and why an industry, formerly well-respected by the public, is considered to be a pariah in the eyes of many sections of society. The theory of social licence and its use in the Australian minerals industry is briefly described and a working definition of “an honest, transparent engagement resulting in a beneficial outcome to all parties before, during and after mining” is adopted throughout the paper. Case studies illustrating examples where mining operations were, and continue to be sustained for decades, provide clear evidence of having a social licence to operate. On the other hand, examples are provided illustrating where poor environmental management practices, tailings dam failures, disputes with landowners, and/or government intervention have resulted in the loss of the social licence and early, unplanned closure. The paradox is that despite the industry's acknowledged contribution to the Australian economy, particularly in times of global ructions such as the GFC and the current coronavirus pandemic, there is considerable antipathy towards the industry by the public. Furthermore, the Australian mining industry's approach to environmental management and sustainable development is regularly used as a model for emerging mining economies. The industry has pioneered remediation and rehabilitation on challenging sites, including prime agricultural land, forests, riverine and beach environments. Successes are rarely acknowledged however but failures are highlighted, by the media, opponents of the industry, and governments. Clearly, the business as usual approach is not enough. Mining industry leaders need to take strong measures to ensure the industry is sustainable and maintains its social licence including eliminating all fatalities and serious injuries, ensuring the safety and stability of tailings storage facilities, accelerating progressive rehabilitation particularly on open cut coal mines, successfully closing mines, and lifting the environmental performance of all mines, not just a few.


title: Factores relacionados con el contagio por SARS-CoV-2 en profesionales de la salud en España. Proyecto SANICOVI

text: ABSTRACT Objective: To describe the factors related to the situation of SARS-CoV-2 transmission identified by health professionals in Spain and to propose prevention strategies. Method: Cross-sectional descriptive study. The population were healthcare professionals working in institutions caring for COVID-19 patients and also confirmed cases of SARS-CoV-2 infection. A questionnaire with sociodemographic, occupational and epidemiological variables was used. Descriptive and bivariate analysis was performed according to the nature of the variables. Results: Twenty-two hundred and thirty questionnaires were analysed on a potential population of 41,239 (5.47%). The diagnosis was made based on a suspicious case (63.4%) and a probable case (12.3%). A study of contacts was carried out at 50.3%. The perception about the availability of protective measures as "always/frequently" were: FPP1 mask 57.3%, gloves 89.5%, soap 95% and hydroalcoholic solution 91.5%. In PPE, FPP2, FPP3 mask, goggles and disposable gowns at around 50%. The availability of protective measures, by field of work, presented significant differences. The average number of patients attended related to the performance of hand hygiene at moment 4 and the perception of performing it correctly at moments 4 and 5. Conclusions: Preliminary data are presented, with variability in the response rate by Autonomous Region. Healthcare professionals infected by SARS-CoV-2 identified the management of the chain of infection transmission, the use and adequacy of protective equipment, as well as the effectiveness of handwashing as factors related to the transmission of the virus among professionals.


title: When there is a pandemic there is no time to waste: should we have hydroxychloroquine in our armoury against COVID-19 infected patients?

text: The current use of chloroquine and/or hydroxychloroquine, a drug currently used to treat autoimmune rheumatic diseases, in treating severe acute respiratory syndrome caused by coronavirus 2 (SARSCoV-2) or COVID-19-infected patients with pneumonia is a matter of intense consideration. We wish to enter the ongoing debate as to whether this well-known drug must be given to Greek COVID-19-infected patients, especially those with pneumonia. Our arguments are based on the existing data and the capacity of the Greek health system to afford potent anti-viral treatments, which are under immense investigation. We propose several suggestions related to treatment of COVID-19 pneumonia with chloroquine/hydroxychloroquine that we think must be taken into consideration to fit the evolving situation of the pandemic in Greece.


title: Coronavirus NSP6 restricts autophagosome expansion

text: Autophagy is a cellular response to starvation that generates autophagosomes to carry long-lived proteins and cellular organelles to lysosomes for degradation. Activation of autophagy by viruses can provide an innate defense against infection, and for (+) strand RNA viruses autophagosomes can facilitate assembly of replicase proteins. We demonstrated that nonstructural protein (NSP) 6 of the avian coronavirus, infectious bronchitis virus (IBV), generates autophagosomes from the ER. A statistical analysis of MAP1LC3B puncta showed that NSP6 induced greater numbers of autophagosomes per cell compared with starvation, but the autophagosomes induced by NSP6 had smaller diameters compared with starvation controls. Small diameter autophagosomes were also induced by infection of cells with IBV, and by NSP6 proteins of MHV and SARS and NSP5, NSP6, and NSP7 of arterivirus PRRSV. Analysis of WIPI2 puncta induced by NSP6 suggests that NSP6 limits autophagosome diameter at the point of omegasome formation. IBV NSP6 also limited autophagosome and omegasome expansion in response to starvation and Torin1 and could therefore limit the size of autophagosomes induced following inhibition of MTOR signaling, as well as those induced independently by the NSP6 protein itself. MAP1LC3B-puncta induced by NSP6 contained SQSTM1, which suggests they can incorporate autophagy cargos. However, NSP6 inhibited the autophagosome/lysosome expansion normally seen following starvation. Taken together the results show that coronavirus NSP6 proteins limit autophagosome expansion, whether they are induced directly by the NSP6 protein, or indirectly by starvation or chemical inhibition of MTOR signaling. This may favor coronavirus infection by compromising the ability of autophagosomes to deliver viral components to lysosomes for degradation.


The COVID‐19 Pandemic Illuminates Persistent and Emerging Disparities among Rural Black Populations


title: Knowledge, Attitude, and Practices Toward COVID-19 in Primary Healthcare Providers: A Cross-Sectional Study from Three Tertiary Care Hospitals of Peshawar, Pakistan

text: An online cross-sectional study was carried out to evaluate the knowledge, attitude, and practice about coronavirus disease 2019 (COVID-19) among primary health care providers (PHPs) at three tertiary care hospital, Peshawar, Pakistan. Data was collected via email and online social media platforms. Statistical package for social science (SPSS) version 25.0 was used for data analysis. Among the total participants (n = 114), 74 (66.7%) were male and 37 (33.3%) were female. The mean scores for knowledge, attitude and practice were 12.7 ± 0.89, 8.9 ± 4.1 and 7.3 ± 1.2, respectively. Most of the participants knew the term COVID-19 and its mode of transmission (90%), signs and symptoms (84%) and risk factors (72%) associated with it. Most of the participants agreed that COVID-19 can be transmitted through coughing and sneezing (74.3%) and 84.6% were in favor that COVID-19 can be prevented by adopting preventive measures. Around 68.8% of the participants disagreed with the use of antibiotics in the prevention of COVID-19. Ninety percent of the respondents were avoiding close contact with the people having cough and flu-like symptoms. Most PHPs had good knowledge, positive attitude and reasonable practices regarding COVID-19. Moreover, focused training programs for PHPs at the Government level can further improve their understanding of risks and preventive strategies related to COVID-19, which will help them to provide appropriate care to their patients as well as to protect themselves from this infection.


title: Safety and Efficacy of 0.5% Carbomer 980 Gel for Treatment of Symptoms of Common Cold: Results of 2 Randomized Trials

text: BACKGROUND: Two studies of intranasal 0.5% carbomer 980 gel were conducted evaluating nasal tolerability in healthy volunteers and safety and efficacy in adults with common cold symptoms. METHODS: Study 1 randomly assigned healthy adults to 0.5% carbomer 980 gel (n = 20) or placebo (n = 10) administered intranasally four times daily for 7 days. Nasal examinations were conducted at baseline and daily throughout the study. The primary endpoint was local nasal tolerability. Study 2 randomly assigned adults with an investigator-confirmed diagnosis of symptomatic common cold to 0.5% carbomer 980 gel (n = 87) or placebo (n = 81), administered intranasally four times daily for 7 days (except for day 1, where subjects who received their first dose mid-day administered only three doses). The primary efficacy endpoint was the average nasal symptom score over days 1‒4 (ANSS(1–4)). Secondary efficacy endpoints included ANSS over days 1‒7 and average total symptom score (ATSS). Adverse events (AEs) were recorded throughout the study. RESULTS: In study 1, subjects assigned to 0.5% carbomer 980 gel had no mucosal grading higher than grade 1B (superficial nasal mucosal erosion) and low incidences of mucosal bleeding and crusting. In study 2, there were no statistically significant differences between treatments for any efficacy endpoints. Active treatment was well-tolerated; the most commonly reported AEs were headache, myalgia, and cough. CONCLUSION: While 0.5% carbomer 980 gel nasal spray demonstrated good local nasal tolerability in healthy volunteers, the spray did not significantly impact the course of infection or resolution of cold symptoms in subjects with common cold.


title: Ebola virus secreted glycoprotein decreases the anti-viral immunity of macrophages in early inflammatory responses

text: Abstract During Ebola virus (EBOV) infection, secreted glycoprotein (sGP) is found in large quantities in the serum of both patients and infected animal models. It is thought to serve as a decoy for anti-EBOV antibodies. Using an in vitro model incorporating treatment of non-infected human THP-1 macrophages with recombinant EBOV sGP, this study sought to examine the impact of sGP upon key macrophage functions. Macrophage polarization and phagocytic capacity of activated macrophages were found to be unaltered by sGP treatment. However, treatment with sGP inhibited macrophage production of the pro-inflammatory cytokines TNFα and IL-6 while the yield of anti-inflammatory cytokine, IL-10, remained intact. Interestingly, the migratory ability of macrophages was also diminished by sGP, potentially due to a decrease in expression of CD11b, a vital macrophage integrin. Thus, EBOV sGP may operate to diminish functional contributions of non-infected macrophages to increase the potential viral dissemination.


title: T cell mediated suppression of neurotropic coronavirus replication in neural precursor cells

text: Abstract Neural precursor cells (NPCs) are the subject of intense investigation for their potential to treat neurodegenerative disorders, yet the consequences of neuroinvasive virus infection of NPCs remain unclear. This study demonstrates that NPCs support replication following infection by the neurotropic JHM strain of mouse hepatitis virus (JHMV). JHMV infection leads to increased cell death and dampens IFN-γ-induced MHC class II expression. Importantly, cytokines secreted by CD4+ T cells inhibit JHMV replication in NPCs, and CD8+ T cells specifically target viral peptide-pulsed NPCs for lysis. Furthermore, treatment with IFN-γ inhibits JHMV replication in a dose-dependent manner. Together, these findings suggest that T cells play a critical role in controlling replication of a neurotropic virus in NPCs, a finding which has important implications when considering immune modulation for NPC-based therapies for treatment of human neurologic diseases.


title: COVID-19 patients and the radiology department – advice from the European Society of Radiology (ESR) and the European Society of Thoracic Imaging (ESTI)

text: ABSTRACT: This document from the European Society of Radiology (ESR) and the European Society of Thoracic Imaging (ESTI) aims to present the main imaging features, and the role of CT scan in the early diagnosis of COVID-19, describing, in particular, the typical findings which make it possible to identify the disease and distinguish it from bacterial causes of infection, and to define which category of patients may benefit from CT imaging. The precautions that must be taken when performing scans to protect radiologists and technologists from infection will be described. The organisational measures that can be taken within radiology departments in order to cope with the influx of patients, while continuing to manage other emergency and time-sensitive activity (e.g. oncology, other infectious diseases etc.), will be discussed. KEY POINTS: • Bilateral ground glass opacities are typical CT manifestations of COVID-19. • Crazy paving and organising pneumonia pattern are seen at a later stage. • Extensive consolidation is associated with a poor prognosis.


title: Chapter Nine Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”

text: Abstract Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle “big data”, provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology. We present how viral sequences can be detected de novo out of current short-read NGS data. Furthermore, we discuss the challenges and applications of viral quasispecies and how secondary structures, commonly shaped by RNA viruses, can be computationally predicted. The phylogenetic analysis of viruses, as another ubiquitous field in virology, forms an essential element of describing viral epidemics and challenges current algorithms. Recently, the first specialized virus-bioinformatic organizations have been established. We need to bring together virologists and bioinformaticians and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology.


Disrupting the Disruption: Using Digital Tools to Support Psychiatry Residency Training in Singapore During the COVID-19 Pandemic


title: SARS-associated Coronavirus Transmission, United States

text: To better assess the risk for transmission of the severe acute respiratory syndrome–associated coronavirus (SARS-CoV), we obtained serial specimens and clinical and exposure data from seven confirmed U.S. SARS patients and their 10 household contacts. SARS-CoV was detected in a day-14 sputum specimen from one case-patient and in five stool specimens from two case-patients. In one case-patient, SARS-CoV persisted in stool for at least 26 days after symptom onset. The highest amounts of virus were in the day-14 sputum sample and a day-14 stool sample. Residual respiratory symptoms were still present in recovered SARS case-patients 2 months after illness onset. Possible transmission of SARS-CoV occurred in one household contact, but this person had also traveled to a SARS-affected area. The data suggest that SARS-CoV is not always transmitted efficiently. Laboratory diagnosis of SARS-CoV infection is difficult; thus, sputum and stool specimens should be included in the diagnostic work-up for SARS-CoV infection.


title: Complete Genome Sequencing of a Novel Strain of Sapelovirus A Circulating in Vietnam

text: Sapelovirus A (SV-A) is currently spreading as an enteric pathogen of pigs worldwide. We isolated SV-A strain XTND/2018 from the small intestine of a dead pig with severe diarrhea in the north of Vietnam and determined the genomic sequence. This is the first report of the genomic sequence of SV-A circulating in Vietnam.


title: Ebola virus disease: The use of fluorescents as markers of contamination for personal protective equipment

text: The recent Ebola virus disease (EVD) outbreak has created interest in personal protective equipment (PPE) content and usage. PPE testing has historically been done by individual component, rather than as a bundle for contact isolation. Fluorescent agents are commonly used in training for infection control techniques. The purpose of our study was to compare 2 PPE bundles and to evaluate the feasibility of fluorescent markers as an assessment tool for PPE effectiveness. Eight healthcare providers volunteered for this preliminary study. Participants were randomized to 1 of 2 PPE bundles that meet current (October 20, 2014) CDC recommendations. One PPE bundle utilized commercial EVD-recommended components. The other PPE bundle used components already available at local hospitals or retail stores. Participants were also randomized to standard or high volume exposures (HVE) to simulate fluid splash. Each participant was assisted in PPE donning and doffing by an experienced trainer. A training mannequin was contaminated with fluorescent agents to simulate bodily fluids. Participants were then given clinical tasks to care for the EVD “patient.” De-gowned participants were examined under “black light” for fluorescence indicative of contamination. One participant in each PPE arm had evidence of contamination. One of the contamination events was suspected during the patient care exercise. The other contamination event was not suspected until black light examination. In spite of a large difference in cost of PPE, the two bundle arms performed similarly. Bundle testing using fluorescent markers could help identify optimal PPE systems.


title: Phages Bearing Affinity Peptides to Bovine Rotavirus Differentiate the Virus from Other Viruses

text: The aim of this study was to identify potential ligands and develop a novel diagnostic test to pathogenic bovine rotavirus (BRV) using phage display technology. The viruses were used as an immobilized target followed by incubation with a 12-mer phage display random peptide library. After five rounds of biopanning, phages had a specific binding activity to BRV were isolated. DNA sequencing indicated that phage displayed peptides HVHPPLRPHSDK, HATNHLPTPHNR or YPTHHAHTTPVR were potential ligands to BRV. Using the specific peptide-expressing phages, we developed a phage-based ELISA to differentiate BRV from other viruses. Compared with quantitative real-time PCR (qPCR), the phage-mediated ELISA was more suitable for the capture of BRV and the detection limitation of this approach was 0.1 µg/ml of samples. The high sensitivity, specificity and low cross-reactivity for the phage-based ELISA were confirmed in receiver operating characteristics (ROC) analysis.


“The Duty to Prevent” during an epidemic situation like 2015 Korean MERS outbreak


title: Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children

text: BACKGROUND: Human bocavirus is a newly discovered parvovirus. Multiple studies have confirmed the presence of human bocavirus1 (HBoV1) in respiratory tract samples of children. The viral load, presentation of single detection and its role as a causative agent of severe respiratory tract infections have not been thoroughly elucidated. METHODS: We investigated the presence of HBoV1 by quantitative polymerase chain reaction (PCR) of nasopharyngeal aspirate specimens from 1229 children hospitalized for respiratory tract infections. The samples were analyzed for 15 respiratory viruses by PCR and 7 respiratory viruses by viral culture. RESULTS: At least one virus was detected in 652 (53.1%) of 1229 children, and two or more viruses were detected in 266 (21.6%) children. HBoV1 was detected in 127 children (10.3%), in which 66/127 (52%) of the cases were the only HBoV1 virus detected. Seasonal variation was observed with a high HBoV1 infection rate in summer. A cutoff value of 10(7) copies/mL was used to distinguish high and low HBoV1 viral loads in the nasopharyngeal aspirates. High viral loads of HBoV1 were noted predominantly in the absence of other viral agents (28/39, 71.8%) whereas there was primarily co-detection in cases of low HBoV1 viral loads (50/88, 56.8%). There were no differences in the clinical symptoms and severity between HBoV1 single detection and co-detection. In cases of HBoV1 single detection, the high viral load group was more prevalent among children with dyspnea and wheezing than was the low viral load group (42.9% vs. 23.7%, P = 0.036; 60.7% vs. 31.6%, P = 0.018). In clinical severity, a significant difference was recorded (25.0% vs. 5.3%, P = 0.003) between high viral load and low viral load groups. Of the HBoV1 positive patients associated with severe respiratory tract infections, 10/18 (55.6%) patients belonged to the HBoV1 high viral load group, and 7/10 (70%) patients had cases of HBoV1 single detection. CONCLUSIONS: HBoV1 at a high viral load is not frequently found in co-detection with other respiratory viruses, and a single detection with a high viral load could be an etiological agent of severe respiratory tract infections. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2334-14-424) contains supplementary material, which is available to authorized users.


title: Colostrum Management for Dairy Calves

text: Colostrum management is the single most important management factor in determining calf health and survival. Additional benefits of good colostrum management include improved rate of gain and future productivity. Successful colostrum management requires producers to provide calves with a sufficient volume of clean, high-quality colostrum within the first few hours of life. This article reviews the process of colostrogenesis and colostrum composition, and discusses key components in developing a successful colostrum management program. In addition, the article discusses approaches for monitoring and proposes new goals for passive immunity in dairy herds.


title: Point-of-care chest ultrasonography as a diagnostic resource for COVID-19 outbreak in nursing homes

text: ABSTRACT Objective Bedside chest ultrasound, when integrated with clinical data, is an accurate tool improving the diagnostic process of many respiratory diseases. This study aims to evaluate the feasibility of a chest ultrasound screening program in nursing homes for detecting coronavirus disease-19 (COVID-19)-related pneumonia and improving the appropriateness of hospital referral of residents. Design Pragmatic, descriptive, feasibility study from April 2nd to April 9th, 2020. Setting and participants: A total of 83 older residents (age 85±8) presenting mild to moderate respiratory symptoms and not previously tested for COVID-19, residing in five nursing homes in Northern Italy. Methods Chest ultrasound was performed at the bedside by a team of hospital specialists with certified expertise in thoracic ultrasonography, following a systematic approach exploring four different areas for each hemithorax, from the anterior and posterior side. Presence of ultrasonographic signs of interstitial pneumonia, including comet-tail artifacts (B-lines) with focal or diffuse distribution, subpleural consolidations and pleural line indentation was detected. The specialist team integrated ultrasound data with clinical and anamnestic information, and gave personalized therapeutic advice for each patient, including hospital referral when needed. Results The most frequent reasons for ultrasound evaluation were fever (63% of participants) and mild dyspnea (40%). Fifty-six patients (67%) had abnormal ultrasound findings. The most common patterns were presence of multiple subpleural consolidations (32 patients) and diffuse B-lines (24 patients), with bilateral involvement. A diagnosis of suspect COVID-19 pneumonia was made in 44 patients, and six of them required hospitalization. Twelve patients had ultrasound patterns suggesting other respiratory diseases, and two patients with normal ultrasound findings were diagnosed with COPD exacerbation. Conclusions and implications In nursing home residents, screening of COVID-19 pneumonia with bedside chest ultrasonography is feasible and may represent a valid diagnostic aid for an early detection of COVID-19 outbreaks and adequate patient management.


title: Antimicrobial Use in the Treatment of Calf Diarrhea

text: Calves with diarrhea often have small intestinal overgrowth with Escherichia coli bacteria, regardless of the inciting cause for the diarrhea, and 30% of systemically ill calves with diarrhea have bacteremia, predominantly because of E coli. Antimicrobial treatment of diarrheic calves should therefore be focused against E coli in the small intestine and blood, the 2 sites of infection. Fecal bacterial culture and antimicrobial susceptibility testing is not recommended in calves with diarrhea because fecal bacterial populations do not accurately reflect small intestinal or blood bacterial populations and because the break points for susceptibility test results have not been validated. Antimicrobial efficacy is therefore best evaluated by the clinical response of a number of calves to treatment, with calves randomly assigned to treatment groups. Amoxicillin, chlortetracycline, neomycin, oxytetracycline, streptomycin, sulfachloropyridazine, sulfamethazine, and tetracycline administered PO are currently labeled in the United States for the treatment of calf diarrhea. On the basis of published evidence for the oral administration of these antimicrobial agents, only amoxicillin can be recommended for the treatment of diarrhea. Dosage recommendations are amoxicillin trihydrate (10 mg/kg PO q12h) or amoxicillin trihydrate‐clavulanate potassium (12.5 mg combined drug/kg PO q12h) for at least 3 days; the latter constitutes extra‐label drug use. Parenteral administration of broad‐spectrum β‐lactam antimicrobials–eftiofur (2.2mg/kg IM orSCq12h) and amoxicillin or ampicillin (10 mg/kg IM q12h)–rpotentiatedsulfonamides(25 mg/kg IV or IM q24h) is recommended for treating calves with diarrhea and systemic illness; both constitute extra‐label drug use. In calves with diarrhea and no systemic illness (normal appetite for milk, no fever), it is recommended that the health of the calf be monitored and that oral or parenteral antimicrobials not be administered.


title: Association between multiple respiratory viral infections and pediatric intensive care unit admission among infants with bronchiolitis

text: Abstract Background It is unclear whether multiple respiratory viral infections are associated with more severe bronchiolitis requiring pediatric intensive care unit (PICU) admission. We aimed to identify the association between multiple respiratory viral infections and PICU admission among infants with bronchiolitis. Methods We performed a 1:1 case-control study enrolling previously healthy full-term infants (≤12 months) with bronchiolitis admitted to the PICU as cases and those to the general pediatric ward as controls from 2015 to 2017. Multiplex polymerase chain reaction (PCR) was used for detection of the respiratory viruses. We summarized the characteristics of infants admitted to the PICU and the general pediatric unit. Multivariable logistic regression analysis was used to fit the association between multiple respiratory viral infections (≥2 strains) and PICU admission. Results A total of 135 infants admitted to the PICU were compared with 135 randomly selected control infants admitted to the general pediatric unit. The PICU patients were younger (median: 2.2 months, interquartile range: 1.3–4.2) than the general ward patients (median: 3.2 months, interquartile range: 1.6–6.4). Respiratory syncytial virus (74.1%), rhinovirus (28.9%), and coronavirus (5.9%) were the most common viruses for bronchiolitis requiring PICU admission. Patients with bronchiolitis admitted to the PICU tended to have multiple viral infections compared with patients on the general ward (23.0% vs. 10.4%, P <0.001). In the multivariable logistic regression analysis, bronchiolitis with multiple viral infections was associated with higher odds of PICU admission (adjusted odds ratio: 2.56, 95% confidence interval: 1.17–5.57, P =0.02). Conclusion Infants with multiviral bronchiolitis have higher odds of PICU admission compared with those with a single or nondetectable viral infection.


title: Prevalence of viral respiratory tract infections in children with asthma

text: Background Previous studies support a strong association between viral respiratory tract infections and asthma exacerbations. The effect of newly discovered viruses on asthma control is less well defined. Objective We sought to determine the contribution of respiratory viruses to asthma exacerbations in children with a panel of PCR assays for common and newly discovered respiratory viruses. Methods Respiratory specimens from children aged 2 to 17 years with asthma exacerbations (case patients, n = 65) and with well-controlled asthma (control subjects, n = 77), frequency matched by age and season of enrollment, were tested for rhinoviruses, enteroviruses, respiratory syncytial virus, human metapneumovirus, coronaviruses 229E and OC43, parainfluenza viruses 1 to 3, influenza viruses, adenoviruses, and human bocavirus. Results Infection with respiratory viruses was associated with asthma exacerbations (63.1% in case patients vs 23.4% in control subjects; odds ratio, 5.6; 95% CI, 2.7- 11.6). Rhinovirus was by far the most prevalent virus (60% among case patients vs 18.2% among control subjects) and the only virus significantly associated with exacerbations (odds ratio, 6.8; 95% CI, 3.2-14.5). However, in children without clinically manifested viral respiratory tract illness, the prevalence of rhinovirus infection was similar in case patients (29.2%) versus control subjects (23.4%, P > .05). Other viruses detected included human metapneumovirus (4.6% in patients with acute asthma vs 2.6% in control subjects), enteroviruses (4.6% vs 0%), coronavirus 229E (0% vs 1.3%), and respiratory syncytial virus (1.5% vs 0%). Conclusion Symptomatic rhinovirus infections are an important contributor to asthma exacerbations in children. Clinical implications These results support the need for therapies effective against rhinovirus as a means to decrease asthma exacerbations.


title: Contrasting Patterns in Mammal–Bacteria Coevolution: Bartonella and Leptospira in Bats and Rodents

text: BACKGROUND: Emerging bacterial zoonoses in bats and rodents remain relatively understudied. We conduct the first comparative host–pathogen coevolutionary analyses of bacterial pathogens in these hosts, using Bartonella spp. and Leptospira spp. as a model. METHODOLOGY/PRINCIPAL FINDINGS: We used published genetic data for 51 Bartonella genotypes from 24 bat species, 129 Bartonella from 38 rodents, and 26 Leptospira from 20 bats. We generated maximum likelihood and Bayesian phylogenies for hosts and bacteria, and tested for coevoutionary congruence using programs ParaFit, PACO, and Jane. Bartonella spp. and their bat hosts had a significant coevolutionary fit (ParaFitGlobal = 1.9703, P≤0.001; m(2) global value = 7.3320, P≤0.0001). Bartonella spp. and rodent hosts also indicated strong overall patterns of cospeciation (ParaFitGlobal = 102.4409, P≤0.001; m(2) global value = 86.532, P≤0.0001). In contrast, we were unable to reject independence of speciation events in Leptospira and bats (ParaFitGlobal = 0.0042, P = 0.84; m(2) global value = 4.6310, P = 0.5629). Separate analyses of New World and Old World data subsets yielded results congruent with analysis from entire datasets. We also conducted event-based cophylogeny analyses to reconstruct likely evolutionary histories for each group of pathogens and hosts. Leptospira and bats had the greatest number of host switches per parasite (0.731), while Bartonella and rodents had the fewest (0.264). CONCLUSIONS/SIGNIFICANCE: In both bat and rodent hosts, Bartonella exhibits significant coevolution with minimal host switching, while Leptospira in bats lacks evolutionary congruence with its host and has high number of host switches. Reasons underlying these variable coevolutionary patterns in host range are likely due to differences in disease-specific transmission and host ecology. Understanding the coevolutionary patterns and frequency of host-switching events between bacterial pathogens and their hosts will allow better prediction of spillover between mammal reservoirs, and ultimately to humans.


title: Regulation of coronaviral poly(A) tail length during infection is not coronavirus species- or host cell-specific

text: It has been demonstrated that the length of the poly(A) tail in the bovine coronavirus (BCoV), which belongs to genus betacoronaviruses, is regulated throughout infection in human rectal tumor-18 (HRT-18) cells, and the length of the poly(A) tail is associated with the efficiency of virus translation. Here, we examined whether the regulation of viral poly(A) tail length is cell-type independent and whether it is a common feature of coronaviruses to assess the significance of the regulation. By ligating head-to-tail viral RNA positive strands and sequencing, we found that (1) the regulation pattern of coronaviral poly(A) tail length in BCoV-infected hamster kidney-21 (BHK-21) cells was similar to that in BCoV-infected HRT-18 cells and (2) the poly(A) tail length of wild-type avian infectious bronchitis virus (IBV) virulent strain IBV-TW1, which is in the genus gammacoronaviruses, varied throughout infection in primary chicken embryo kidney (CEK) cells and in the tracheas of 1-day-old chicks. Interestingly, the poly(A) tail length variation was similarly found in the avirulent IBV strain H120 in CEK cells, although the overall poly(A) tail length was shorter for this virus. The results suggest that the regulation of coronaviral poly(A) tail length during infection may be a common feature among coronaviruses and can occur in a noncancerous cell line (BHK-21 cells), primary cell culture (CEK cells), and living system (chickens), further reinforcing the biological significance of this regulation during coronavirus infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11262-014-1103-7) contains supplementary material, which is available to authorized users.


title: Influenza C infections in Western Australia and Victoria from 2008 to 2014

text: BACKGROUND: Influenza C is usually considered a minor cause of respiratory illness in humans with many infections being asymptomatic or clinically mild. Large outbreaks can occur periodically resulting in significant morbidity. OBJECTIVES: This study aimed at analyzing the available influenza C clinical samples from two widely separated states of Australia, collected over a 7‐year period and to compare them with influenza C viruses detected in other parts of the world in recent years. PATIENTS/METHODS: Between 2008 and 2014, 86 respiratory samples that were influenza C positive were collected from subjects with influenza‐like illness living in the states of Victoria and Western Australia. A battery of other respiratory viruses were also tested for in these influenza C‐positive samples. Virus isolation was attempted on all of these clinical samples, and gene sequencing was performed on all influenza C‐positive cultures. RESULTS AND CONCLUSIONS: Detections of influenza C in respiratory samples were sporadic in most years studied, but higher rates of infection occurred in 2012 and 2014. Many of the patients with influenza C had coinfections with other respiratory pathogens. Phylogenetic analysis of the full‐length hemagglutinin–esterase–fusion (HE) gene found that most of the viruses grouped in the C/Sao Paulo/378/82 clade with the remainder grouping in the C/Kanagawa/1/76 clade.


title: Achieve Research Continuity During Social Distancing by Rapidly Implementing Individual and Group Videoconferencing with Participants: Key Considerations, Best Practices, and Protocols

text: The novel coronavirus has upended many traditional research procedures as universities and other research entities have closed to activate social distancing. Some social and behavioral research activities (e.g. data analysis, manuscript preparation) can be continued from other environments with appropriate security protocols in place. For studies involving in-person interactions, continuity may be more difficult. Phone-based interactions provide a low-tech solution that may suffice in some cases. Yet, videoconferencing platforms can nearly replicate in-person interactions, activating both auditory and visual senses and potentially resulting in more substantial engagement. Staff can meet with participants individually or in groups, each seeing and hearing one another in real time. This paper provides guidance for researchers transitioning in-person assessments and interventions to a synchronous videoconferencing platform. Best practices, key considerations, examples from the field, and sample protocols are presented to ease transition for ongoing studies and maximize the potential of videoconferencing—and social distancing. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10461-020-02837-x) contains supplementary material, which is available to authorized users.


title: Is the Mortality Trend of Ischemic Heart Disease by the GBD2013 Study in China Real?

text: To determine the reason for the different mortality trends of ischemic heart disease (IHD) for China between Global Burden of Disease (GBD) 2010 and GBD2013, and to improve garbage code (GC) redistribution. All data were obtained from the disease surveillance points system, and two proportions for assigning chronic pulmonary heart disease (PHD) as GC to IHD were from GBD2010 and GBD2013, which were different for years before 2004. By using the GBD2013 approach, the age-standard mortality rate (ASMR) increased by 100.21% in 1991, 44.81% in 1996, and 42.47% in 2000 in comparison with the GBD2010 approach. The different methods of chronic PHD redistribution impacted the trend of IHD mortality, which elevated it in the earlier 1990s by using the GBD2013 approach. Thus, improving the redistribution of GC as a key step in mortality statistics is important.


Life in Hanoi during the Coronavirus Pandemic


Comment on “Response to COVID-19 in Breast Imaging”


title: Multiplex detection and dynamics of IgG antibodies to SARS-CoV2 and the highly pathogenic human Coronaviruses SARS-CoV and MERS-CoV

text: BACKGROUND: Knowledge of the COVID-19 epidemic extent and the level of herd immunity is urgently needed to help manage this pandemic. METHODS: We used a panel of 167 samples (77 pre-epidemic and 90 COVID-19 seroconverters) and SARS-CoV1, SARS-CoV2 and MERS-CoV Spike and/or Nucleopcapsid (NC) proteins to develop a high throughput multiplex screening assay to detect IgG antibodies in human plasma. Assay performances were determined by ROC curves analysis. A subset of the COVID-19+ samples (n = 36) were also tested by a commercial NC-based ELISA test and the results compared with those of the novel assay. RESULTS: On samples collected ≥14 days after symptoms onset, the accuracy of the assay is 100% (95% CI: 100-100) for the Spike antigen and 99.9% (95% CI:99.7-100) for NC. By logistic regression, we estimated that 50% of the patients have seroconverted at 5.7 ± 1.6; 5.7 ± 1.8 and 7.9 ± 1.0 days after symptoms onset against Spike, NC or both antigens, respectively and all have seroconverted two weeks after symptoms onset. IgG titration in a subset of samples showed that early phase samples present lower IgG titers than those from later phase. IgG to SARS-CoV2 NC cross-reacted at 100% with SARS-CoV1 NC. Twenty-nine of the 36 (80.5%) samples tested were positive by the commercial ELISA while 31/36 (86.1%) were positive by the novel assay. CONCLUSIONS: Our assay is highly sensitive and specific for the detection of IgG antibodies to SARS-CoV2 proteins, suitable for high throughput epidemiological surveys. The novel assay is more sensitive than a commercial ELISA.


title: A Scientometric Analysis of Global Health Research

text: With the development and deepening of the process of global integration, global health is gaining increasing attention. An increasing number of studies have examined global health from diverse perspectives to promote the realization of global public health. The purpose of this research is to systematically and comprehensively evaluate the knowledge structure, knowledge domain, and evolution trend in the field of global health research. Based on the 14,692 document data retrieved from Web of Science Core Collection from 1996 to 2019, this article carried out a visual analysis of global health research from the perspective of scientific output characteristics, scientific research cooperation networks, keywords, and highly cited literature. The results show that scholars’ interest in global health research is increasing, especially after the outbreak of SARS. USA, England, Canada, Australia, and China have the most prominent contributions to global health research. Significant authors, high impact journals and core institutions also identified. The study found that “global health governance”, “global health diplomacy”, “medical education”, “global health education” and “antimicrobial resistance” are the research frontiers and hot spots. This study provides an overview and valuable guidance for researchers and related personnel to find the research direction and practice of global health.


title: Pathogen reduction of SARS-CoV-2 virus in plasma and whole blood using riboflavin and UV light

text: BACKGROUND: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has recently been identified as the causative agent for Coronavirus Disease 2019 (COVID-19). The ability of this agent to be transmitted by blood transfusion has not been documented, although viral RNA has been detected in serum. Exposure to treatment with riboflavin and ultraviolet light (R + UV) reduces blood-borne pathogens while maintaining blood product quality. Here, we report on the efficacy of R + UV in reducing SARS-CoV-2 infectivity when tested in human plasma and whole blood products. STUDY DESIGN AND METHODS: SARS-CoV-2 (isolate USA-WA1/2020) was used to inoculate plasma and whole blood units that then underwent treatment with riboflavin and UV light (Mirasol Pathogen Reduction Technology System, Terumo BCT, Lakewood, CO). The infectious titers of SARS-CoV-2 in the samples before and after R + UV treatment were determined by plaque assay on Vero E6 cells. Each plasma pool (n = 9) underwent R + UV treatment performed in triplicate using individual units of plasma and then repeated using individual whole blood donations (n = 3). RESULTS: Riboflavin and UV light reduced the infectious titer of SARS-CoV-2 below the limit of detection for plasma products at 60–100% of the recommended energy dose. At the UV light dose recommended by the manufacturer, the mean log reductions in the viral titers were ≥ 4.79 ± 0.15 Logs in plasma and 3.30 ± 0.26 in whole blood units. CONCLUSION: Riboflavin and UV light effectively reduced the titer of SARS-CoV-2 to the limit of detection in human plasma and by 3.30 ± 0.26 on average in whole blood. Two clades of SARS-CoV-2 have been described and questions remain about whether exposure to one strain confers strong immunity to the other. Pathogen-reduced blood products may be a safer option for critically ill patients with COVID-19, particularly those in high-risk categories.