title: Detection of viruses identified recently in children with acute wheezing

text: The etiologic role of recently identified respiratory viruses for acute wheezing in children is not yet clear. The purpose of this study was to investigate the prevalence of recently identified viruses, including human metapneumovirus (hMPV), human bocavirus (hBoV), human coronavirus NL63 (hCoV‐NL63), and human coronavirus HKU1 (hCoV‐HKU1) in children with acute wheezing. Viral etiology was identified in 231 children hospitalized with acute wheezing, aged from 1 month to 5 years. Viral antigens for common respiratory viruses were detected by IFA or multiplex PCR. RT‐PCR was used to detect respiratory rhinoviruses, hCoV‐NL63, hCoV‐HKU1, and hMPV. PCR assays for hBoV DNA were performed using the primer sets for noncapsid protein (NP1) and nonstructural protein (NS1) genes. Viruses were found in 61.5% (142/231) of the study population and a single virus was detected in 45.5% (105/231) of the study population. Rhinovirus (33.3%), human respiratory syncytial virus (hRSV; 13.8%), and hBoV (13.8%) were the most frequently detected viruses. hMPV and hCoV‐NL63 were detected in 7.8% and 1.3% of wheezing children, respectively. HCoV‐HKU1 was not detected. In 16.0% of the study population, more than one virus was detected. In children with acute wheezing, rhinovirus, hRSV, and hBoV were most frequently detected. Further studies including healthy control subjects are needed to define the clinical significance of hBoV in acute wheezing. J. Med. Virol. 79: 1238–1243, 2007. © 2007 Wiley‐Liss, Inc.


title: Hospitalization Risk Due to Respiratory Illness Associated with Genetic Variation at IFITM3 in Patients with Influenza A(H1N1)pdm09 Infection: A Case-Control Study

text: BACKGROUND: Recent studies suggest an association between the Interferon Inducible Transmembrane 3 (IFITM3) rs12252 variant and the course of influenza infection. However, it is not clear whether the reported association relates to influenza infection severity. The aim of this study was to estimate the hospitalization risk associated with this variant in Influenza Like Illness (ILI) patients during the H1N1 pandemic influenza. METHODS: A case-control genetic association study was performed, using nasopharyngeal/oropharyngeal swabs collected during the H1N1 pandemic influenza. Laboratory diagnosis of influenza infection was performed by RT-PCR, the IFITM3 rs12252 was genotyped by RFLP and tested for association with hospitalization. Conditional logistic regression was performed to calculate the confounder-adjusted odds ratio of hospitalization associated with IFITM3 rs12252. RESULTS: We selected 312 ILI cases and 624 matched non-hospitalized controls. Within ILI Influenza A(H1N1)pdm09 positive patients, no statistical significant association was found between the variant and the hospitalization risk (Adjusted OR: 0.73 (95%CI: 0.33–1.50)). Regarding ILI Influenza A(H1N1)pdm09 negative patients, CT/CC genotype carriers had a higher risk of being hospitalized than patients with TT genotype (Adjusted OR: 2.54 (95%CI: 1.54–4.19)). CONCLUSIONS: The IFITM3 rs12252 variant was associated with respiratory infection hospitalization but not specifically in patients infected with Influenza A(H1N1)pdm09.


title: Yu Ping Feng San, an Ancient Chinese Herbal Decoction Containing Astragali Radix, Atractylodis Macrocephalae Rhizoma and Saposhnikoviae Radix, Regulates the Release of Cytokines in Murine Macrophages

text: Yu Ping Feng San (YPFS), a Chinese herbal decoction, is composed of Astragali Radix (AR; Huangqi), Atractylodis Macrocephalae Rhizoma (AMR; Baizhu) and Saposhnikoviae Radix (SR; Fangfeng) in a weight ratio of 1∶2∶1. Clinically, YPFS has been widely used to regulate immune functions; however, the action mechanism of it is not known. Here, we addressed this issue by providing detail analyses of chemical and biological properties of YPFS. By using rapid resolution liquid chromatography coupled with mass spectrometry, fifteen chemicals deriving from different herbs of YPFS were determined, and which served as a control for the standardization of the herbal extract of YPFS. In general, the amounts of chosen chemical markers were higher in a preparation of YPFS as compared to that of single herb or two-herb compositions. In order to reveal the immune functions of YPFS, the standardized extract was applied onto cultured murine macrophages. The treatment of YPFS stimulated the mRNA and protein expressions of pro-inflammatory cytokines via activation of NF-κB by enhancing IκBα degradation. In contrast, the application of YPFS suppressed the expressions of pro-inflammatory cytokines significantly in the lipopolysaccharide (LPS)-induced chronic inflammation model. In addition, YPFS could up regulate the phagocytic activity in cultured macrophages. These results therefore supported the bi-directional immune-modulatory roles of YPFS in regulating the releases of cytokines from macrophages.


title: Evolutionary implications of genetic variations in the S1 gene of infectious bronchitis virus

text: Abstract The large number of phenotypically distinct strains of infectious bronchitis virus (IBV) provide a broad genetic background for examining naturally occurring coronavirus variation. Comparisons of the published nucleotide sequence of S1 genes of strains isolated in Europe, Japan and the USA and four additional American strains described in this report identified 4 genetically distinct groups. The Dutch group was the most divergent sharing only about 60% identity with the American, Mass and European groups which were about 80% homologous with each other. Whereas the strains within the Mass, European and Dutch strains were at least 95% homologous, the strains within the American group were most variable, sharing about 80% identity. The hypervariable region (HVR) which tended to correlate with serotype extended from amino acid residue 53 to 148. In addition to the previously described putative recombination events in the S1 gene of PP14 and SE17, we have now described similar shifts in homology in the corresponding gene of the Gray, Holte, 6/82 (European strain), and Iowa strains. Although minor cross-over sites were identified in the more conserved 3' end at approximately nt 1000 and 1400, a frequently used hot-spot for recombination extended from nt 25 to a region immediately upstream of, but not including, the hypervariable region (HVR). In addition to point mutations, deletions, and insertions, recombination often involving Mass-like and Ark-like sequences, is a commonly used mechanism responsible for the evolution of IBV.


title: Effect of siRNA mediated suppression of signaling lymphocyte activation molecule on replication of peste des petits ruminants virus in vitro

text: Abstract Signaling lymphocyte activation molecule (SLAM) expression was inhibited in B95a cell line using siRNA and the effect of SLAM inhibition on peste des petits ruminants virus (PPRV) replication and infectivity titre was studied. SLAM suppression was assessed using real-time PCR and flow cytometry to confirm suppression at the m-RNA and protein levels, respectively. Three chemically synthesized siRNAs were transfected individually using oligofectamine into B95a cell line. This resulted in SLAM suppression from 48 to 454-folds, in comparison to the untransfected B95a cell line. When the SLAM suppressed B95a cell line was infected with PPRV, replication was reduced by 12–143-folds and virus titre was reduced from log10 1.09 to 2.28. siRNA 3 showed the most potent inhibition of SLAM expression both at m-RNA and protein levels. This also caused the maximum reduction of virus replication and virus titre. A 100-fold reduction in PPRV titres was seen in anti-SLAM antibody neutralized B95a cell line. This further confirms that SLAM is one of the (co) receptors for PPRV. However, the presence of other putative virus receptor(s) is/are not ruled out.


title: Exacerbación de la EPOC

text: Resumen Las exacerbaciones de la enfermedad pulmonar obstructiva crónica (EPOC) se consideran episodios de inestabilidad que favorecen la progresión de la enfermedad, disminuyen la calidad de vida del paciente, aumentan el riesgo de defunción y son la causa de un consumo significativo de recursos sanitarios. Estas exacerbaciones se deben a infecciones bacterianas y virales, y a factores estresantes medioambientales, pero otras enfermedades concomitantes como las cardiopatías, otras enfermedades pulmonares (como la embolia pulmonar, la aspiración o el neumotórax) y otros procesos sistémicos, pueden desencadenar o complicar estas agudizaciones. En la fisiopatología de las exacerbaciones los dos factores que más influyen son la hiperinsuflación dinámica y la inflamación local y sistémica. El tratamiento farmacológico en la mayoría de los pacientes incluye broncodilatadores de acción corta, corticoides sistémicos y antibióticos. La insuficiencia respiratoria hipoxémica requiere oxigenoterapia controlada y en la insuficiencia respiratoria hipercápnica la ventilación con presión positiva no invasiva puede permitir ganar tiempo hasta que otros tratamientos empiecen a funcionar y, así, evitar la intubación endotraqueal. El uso de ventilación mecánica no invasiva nunca debe retrasar la intubación si ésta está indicada. Los criterios de alta hospitalaria se basan en la estabilización, tanto clínica como gasométrica, y en la capacidad del paciente para poder controlar la enfermedad en su domicilio. La hospitalización domiciliaria puede ser una opción de tratamiento de la exacerbación de la EPOC con eficacia equivalente a la hospitalización convencional. Abstract Exacerbations of chronic obstructive pulmonary disease (COPD) are considered to be episodes of instability that favor disease progression, reduce quality of life, increase the risk of death and cause substantial healthcare resource use. These exacerbations are due to bacterial and viral infections and environmental stressors. However, other concomitant diseases such as heart disease, other lung diseases (e.g. pulmonary embolism, aspiration or pneumothorax) and other systemic processes can trigger or complicate these exacerbations. The two factors with the greatest influence on the physiopathology of exacerbations are dynamic overinflation and local and systemic inflammation. In most patients, drug treatment includes short-acting bronchodilators, systemic corticosteroids and antibiotics. Hypoxemic respiratory failure requires controlled oxygen therapy. In hypercapnic respiratory failure, non-invasive positive pressure ventilation may allow time to be gained until other treatments begin to take effect and can thus avoid endotracheal intubation. The use of non-invasive mechanical ventilation should never delay intubation, if indicated. Hospital discharge criteria are based on both clinical and gasometric stabilization and on the patient's ability to manage his or her disease at home. Hospitalization at home can be a treatment option in COPD exacerbations and is as effective as conventional hospitalization.


title: SARS-CoV ORF1b-encoded nonstructural proteins 12–16: Replicative enzymes as antiviral targets

text: Abstract The SARS (severe acute respiratory syndrome) pandemic caused ten years ago by the SARS-coronavirus (SARS-CoV) has stimulated a number of studies on the molecular biology of coronaviruses. This research has provided significant new insight into many mechanisms used by the coronavirus replication-transcription complex (RTC). The RTC directs and coordinates processes in order to replicate and transcribe the coronavirus genome, a single-stranded, positive-sense RNA of outstanding length (∼27–32kilobases). Here, we review the up-to-date knowledge on SARS-CoV replicative enzymes encoded in the ORF1b, i.e., the main RNA-dependent RNA polymerase (nsp12), the helicase/triphosphatase (nsp13), two unusual ribonucleases (nsp14, nsp15) and RNA-cap methyltransferases (nsp14, nsp16). We also review how these enzymes co-operate with other viral co-factors (nsp7, nsp8, and nsp10) to regulate their activity. These last ten years of research on SARS-CoV have considerably contributed to unravel structural and functional details of one of the most fascinating replication/transcription machineries of the RNA virus world. This paper forms part of a series of invited articles in Antiviral Research on “From SARS to MERS: 10years of research on highly pathogenic human coronaviruses”.


title: Tele(oral)medicine: A new approach during the COVID‐19 crisis

text: The recent COVID-19 pandemic and state's "Shelter in place" guidelines have restricted patient's access to dental services, including oral medicine, as well as continuity of clinical education for oral medicine residents. This has required immediate attention from clinicians and educators.


title: Generation and Characterization of Eptesicus fuscus (Big brown bat) kidney cell lines immortalized using the Myotis polyomavirus large T-antigen

text: Abstract It is speculated that bats are important reservoir hosts for numerous viruses, with 27 viral families reportedly detected in bats. Majority of these viruses have not been isolated and there is little information regarding their biology in bats. Establishing a well-characterized bat cell line supporting the replication of bat-borne viruses would facilitate the analysis of virus-host interactions in an in vitro model. Currently, few bat cell lines have been developed and only Tb1-Lu, derived from Tadarida brasiliensis is commercially available. Here we describe a method to establish and immortalize big brown bat (Eptesicus fuscus) kidney (Efk3) cells using the Myotis polyomavirus T-antigen. Subclones of this cell line expressed both epithelial and fibroblast markers to varying extents. Cell clones expressed interferon beta in response to poly(I:C) stimulation and supported the replication of four different viruses, namely, vesicular stomatitis virus (VSV), porcine epidemic diarrhea coronavirus (PED-CoV), Middle-East respiratory syndrome coronavirus (MERS-CoV) and herpes simplex virus (HSV). To our knowledge, this is the first bat cell line from a northern latitude insectivorous bat developed using a novel technology. The cell line has the potential to be used for isolation of bat viruses and for studying virus-bat interactions in culture.


title: Funding of drugs: do vaccines warrant a different approach?

text: Summary Vaccines have features that require special consideration when assessing their cost-effectiveness. These features are related to herd immunity, quality-of-life losses in young children, parental care and work loss, time preference, uncertainty, eradication, macroeconomics, and tiered pricing. Advisory committees on public funding for vaccines, or for pharmaceuticals in general, should be knowledgable about these special features. We discuss key issues and difficulties in decision making for vaccines against rotavirus, human papillomavirus, varicella-zoster virus, influenza virus, and Streptococcus pneumoniae. We argue that guidelines for economic evaluation should be reconsidered generally to recommend (1) modelling options for the assessment of interventions against infectious diseases; (2) a wider perspective to account for impacts on third parties, if relevant; (3) a wider scope of costs than health-care system costs alone, if appropriate; and (4) alternative discounting techniques to explore social time preference over long periods.


title: Casualties of war: the infection control assessment of civilians transferred from conflict zones to specialist units overseas for treatment

text: Summary The casualties of global conflict attract media attention and sympathy in public, governmental, and non-governmental circles. Hospitals in developed countries offering specialist reconstructive or tertiary services are not infrequently asked to accept civilian patients from overseas conflict for complex surgical procedures or rehabilitation. Concern about the infection prevention and control risks posed by these patients, and the lack of a good evidence base on which to base measured precautions, means that the precautionary principle of accepting zero risk is usually followed. The aim of this article is to highlight infection control considerations that may be required when treating casualties from overseas conflict, based partly on our own experience. Currently there is a lack of published evidence and national consensus on how to manage these patients. The precautionary principle requires that there is an ongoing search for evidence and knowledge that can be used to move towards more traditional risk management. We propose that only by gathering the experiences of the many individual hospitals that have each cared for small numbers of such patients can such evidence and knowledge be assimilated.


title: Network Analysis of MERS Coronavirus within Households, Communities, and Hospitals to Identify Most Centralized and Super-Spreading in the Arabian Peninsula, 2012 to 2016

text: Contact history is crucial during an infectious disease outbreak and vital when seeking to understand and predict the spread of infectious diseases in human populations. The transmission connectivity networks of people infected with highly contagious Middle East respiratory syndrome coronavirus (MERS-CoV) in Saudi Arabia were assessed to identify super-spreading events among the infected patients between 2012 and 2016. Of the 1379 MERS cases recorded during the study period, 321 (23.3%) cases were linked to hospital infection, out of which 203 (14.7%) cases occurred among healthcare workers. There were 1113 isolated cases while the number of recorded contacts per MERS patient is between 1 (n=210) and 17 (n=1), with a mean of 0.27 (SD = 0.76). Five super-important nodes were identified based on their high number of connected contacts worthy of prioritization (at least degree of 5). The number of secondary cases in each SSE varies (range, 5–17). The eigenvector centrality was significantly (p < 0.05) associated with place of exposure, with hospitals having on average significantly higher eigenvector centrality than other places of exposure. Results suggested that being a healthcare worker has a higher eigenvector centrality score on average than being nonhealthcare workers. Pathogenic droplets are easily transmitted within a confined area of hospitals; therefore, control measures should be put in place to curtail the number of hospital visitors and movements of nonessential staff within the healthcare facility with MERS cases.


title: Virus-like particles as a highly efficient vaccine platform: Diversity of targets and production systems and advances in clinical development

text: Virus-like particles (VLPs) are a class of subunit vaccines that differentiate themselves from soluble recombinant antigens by stronger protective immunogenicity associated with the VLP structure. Like parental viruses, VLPs can be either non-enveloped or enveloped, and they can form following expression of one or several viral structural proteins in a recombinant heterologous system. Depending on the complexity of the VLP, it can be produced in either a prokaryotic or eukaryotic expression system using target-encoding recombinant vectors, or in some cases can be assembled in cell-free conditions. To date, a wide variety of VLP-based candidate vaccines targeting various viral, bacterial, parasitic and fungal pathogens, as well as non-infectious diseases, have been produced in different expression systems. Some VLPs have entered clinical development and a few have been licensed and commercialized. This article reviews VLP-based vaccines produced in different systems, their immunogenicity in animal models and their status in clinical development.


Inflammatory Bowel Disease and COVID-19—“Preventive” Sick Certificates as a Frequent Coping Strategy in the Face of the Pandemic


title: Asthma and COVID‐19 in children – a systematic review and call for data

text: RATIONALE: Whether asthma constitutes a risk factor for COVID‐19 is unclear. Here we aimed to assess whether asthma, the most common chronic disease in children, is associated with higher COVID‐19 risk or severity in pediatric populations. METHODS: We performed a systematic literature search in three stages: First, we reviewed PubMed, EMBASE and CINAHL for systematic reviews of SARS‐CoV‐2 and COVID‐19 in pediatric populations, and reviewed their primary articles; second, we searched PubMed for studies on COVID‐19 or SARS‐CoV‐2 and asthma/wheeze, and evaluated whether the resulting studies included pediatric populations; third, we repeated the second search in BioRxiv.org and MedRxiv.org to find pre‐prints that may have information on pediatric asthma. RESULTS: In the first search, eight systematic reviews were found, of which five were done in pediatric populations; none of the 67 primary studies included data on pediatric asthma as a comorbidity for COVID‐19. In the second search, we found 34 results in PubMed, of which five reported asthma in adults, but none included data on children. In the third search, 25 pre‐prints in MedRxiv included data on asthma, but none on children. We found one report by the U.S. CDC stating that 40/345 (~11.5%) children with data on chronic conditions had “chronic lung diseases including asthma”, and one from a tertiary hospital in New York that reported asthma in 11/46 (~23.9%) children hospitalized for COVID‐19. CONCLUSION: There is scarcely any data on whether childhood asthma (or other pediatric respiratory diseases) constitute risk factors for SARS‐CoV‐2 infection or COVID‐19 severity. Studies are needed that go beyond counting the number of cases in the pediatric age range. This article is protected by copyright. All rights reserved.


title: Viruses as Quasispecies: Biological Implications

text: During viral infections, the complex and dynamic distributions of variants, termed viral quasispecies, play a key role in the adaptability of viruses to changing environments and the fate of the population as a whole. Mutant spectra are continuously and avoidably generated during RNA genome replication, and they are not just a by-product of error-prone replication, devoid of biological relevance. On the contrary, current evidence indicates that mutant spectra contribute to viral pathogenesis, can modulate the expression of phenotypic traits by subpopulations of viruses, can include memory genomes that reflect the past evolutionary history of the viral lineage, and, furthermore, can participate in viral extinction through lethal mutagenesis. Also, mutant spectra are the target on which selection and random drift act to shape the long-term evolution of viruses. The biological relevance of mutant spectra is the central topic of this chapter.


Reining in the CD8+ T cell: Respiratory virus infection and PD-1-mediated T-cell impairment


Nursing's Response to COVID-19: Lessons Learned from SARS in Taiwan


title: Detection of Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella spp. in clinical specimens using a single-tube multiplex real-time PCR assay

text: Abstract A multiplex real-time PCR assay for the detection of Mycoplasma pneumoniae (MP181), Chlamydia (Chlamydophila) pneumoniae (CP-Arg), Legionella spp. (Pan-Leg), and the human RNase P (RNase P) gene was developed for rapid testing of atypical bacterial respiratory pathogens in clinical specimens. This method uses 4 distinct hydrolysis probes to detect 3 leading causes of community-acquired pneumonia. The assay was evaluated for specificity and sensitivity by testing against 35 related organisms, a dilution series of each specific target and 197 clinical specimens. Specificity testing demonstrated no cross-reactivity. A comparison to previously validated singleplex real-time PCR assays for each agent was also performed. The analytical sensitivity for specific pathogen targets in both the singleplex and multiplex was identical (50 fg), while efficiencies ranged from 82% to 97% for the singleplex assays and from 90% to 100% for the multiplex assay. The clinical sensitivity of the multiplex assay was improved for the Pan-Leg and CP-Arg targets when compared to the singleplex. The MP181 assay displayed equivalent performance. This multiplex assay provides an overall improvement in the diagnostic capability for these agents by demonstrating a sensitive, high-throughput and rapid method. This procedure may allow for a practical and efficient means to test respiratory clinical specimens for atypical pneumonia agents in health care settings and facilitate an appropriate public health response to outbreaks.


title: Development of a fully integrated microfluidic system for sensing infectious viral disease

text: An active micromixer system utilizing the magnetic force was developed and examined for its ability to facilitate the mixing of more than two fluid flows. The mixing performance of the active micromixer was evaluated in aqueous–aqueous systems including dyes for visual observation. A complete analytical microfluidic system was developed by integrating various functional modules into a single chip, thus allowing cell lysis, sample preparation, purification of intracellular molecules, and subsequent analysis. Upon loading the cell samples and lysis solution into the mixing chamber, the integrated microfluidic device allows efficient cell disruption by rotation of a micromagnetic disk and control of mixing time using the Teflon‐coated hydrophobic film as a microvalve. This inflow is followed by separating the cell debris and contaminated proteins from the cell lysate sample using the acrylamide (AAm)‐functionalized SPE. The inflow of partially purified cell lysate sample containing the gold binding polypeptide (GBP)‐fusion protein was bound onto the gold micropatterns by means of its metal binding affinity. The GBP‐fusion method allows immobilization of proteins in bioactive forms onto the gold surface without surface modification suitable for studying antigen–antibody interaction. It was used for the detection of severe acute respiratory syndrome (SARS), an infectious viral disease, as an example case.


title: MULTIPRED2: a computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles

text: MULTIPRED2 is a computational system for facile prediction of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR molecules. It enables prediction of peptide binding to products of individual HLA alleles, combination of alleles, or HLA supertypes. NetMHCpan and NetMHCIIpan are used as prediction engines. The 13 HLA Class I supertypes are A1, A2, A3, A24, B7, B8, B27, B44, B58, B62, C1, and C4. The 13 HLA Class II DR supertypes are DR1, DR3, DR4, DR6, DR7, DR8, DR9, DR11, DR12, DR13, DR14, DR15, and DR16. In total, MULTIPRED2 enables prediction of peptide binding to 1077 variants representing 26 HLA supertypes. MULTIPRED2 has visualization modules for mapping promiscuous T-cell epitopes as well as those regions of high target concentration – referred to as T-cell epitope hotspots. Novel graphic representations are employed to display the predicted binding peptides and immunological hotspots in an intuitive manner and also to provide a global view of results as heat maps. Another function of MULTIPRED2, which has direct relevance to vaccine design, is the calculation of population coverage. Currently it calculates population coverage in five major groups in North America. MULTIPRED2 is an important tool to complement wet-lab experimental methods for identification of T-cell epitopes. It is available at http://cvc.dfci.harvard.edu/multipred2/.


title: Public antibodies to malaria antigens generated by two LAIR1 insertion modalities

text: We previously described two donors in whom the extracellular domain of LAIR1, a collagen-binding inhibitory receptor encoded on chromosome 191, was inserted between the V and the DJ segments of an antibody. This insertion generated, through somatic mutations, broadly reactive antibodies against RIFINs, a type of variant antigen expressed on the surface of Plasmodium falciparum-infected erythrocytes (IEs)2. To investigate how frequently such antibodies are produced in response to malaria infection, we screened plasma from two large cohorts of individuals living in malaria-endemic regions. We report that 5-10% of malaria-exposed individuals, but none of the European blood donors tested, have high levels of LAIR1-containing antibodies that dominate the response to IEs without conferring enhanced protection against febrile malaria. By analyzing the antibody-producing B cell clones at the protein, cDNA and gDNA level, we characterized additional LAIR1 insertions between the V and DJ segments and discovered a second insertion modality whereby the LAIR1 exon encoding the extracellular domain and flanking intronic sequences are inserted into the switch region. By exon shuffling, this mechanism leads to the production of bispecific antibodies in which the LAIR1 domain is precisely positioned at the elbow between the VH and CH1 domains. Additionally, in one donor the gDNA encoding the VH and CH1 domains was deleted, leading to the production of a camel-like LAIR1-containing antibody. Sequencing of the switch regions of memory B cells from European blood donors revealed frequent templated inserts originating from transcribed genes that, in rare cases, comprised exons with orientation and frame compatible with expression. Collectively, these results reveal different modalities of LAIR1 insertion that lead to public and dominant antibodies against IEs and suggest that insertion of templated DNA represents an additional mechanism of antibody diversification that can be selected in the immune response against pathogens and exploited for B cell engineering.


A very rare presentation of miliary tuberculosis in mid-trimester pregnancy masquerading as sepsis and severe acute respiratory syndrome Category: Clinical lesson


title: Prospective comparison of RT-PCR/ESI-MS to Prodesse ProFlu Plus and Cepheid GenXpert for the detection of Influenza A and B viruses

text: RT-PCR/ESI-MS has previously demonstrated the capability to detect and identify respiratory viral pathogens in nasopharyngeal swabs. This study expands on previous research by performing a prospective evaluation of RT-PCR/ESI-MS to detect and identify Influenza A and B viruses compared to Prodesse ProFlu Plus and combined ProFlu Plus and Cepheid Xpert Flu. ProFlu Plus was also used as a gold standard for comparison for respiratory syncytial virus detection. Using ProFlu Plus as a gold standard, RT-PCR/ESI-MS had sensitivity and specificity of 82.1% (23/28) and 100% (258/258), respectively, for Influenza A, 100% (16/16) and 99.6% (269/270), respectively for Influenza B, and 88.6% (39/44) and 99.6% (241/242) for any Influenza virus. Using matching results from ProFlu Plus and Xpert Flu as a gold standard, RT-PCR/ESI-MS had 85.2% (23/27) and 100% (259/259) sensitivity and specificity respectively for Influenza A, 100% (14/14) and 99.6% (270/272), respectively for Influenza B virus. Overall, RT-PCR/ESI-MS was not as sensitive as the combined gold standard of ProFlu Plus and Xpert Flu, although it has the capability of detecting other respiratory viruses.


title: Assessment of Proficiency of N95 Mask Donning Among the General Public in Singapore

text: This cross-sectional study examines factors associated with proper use of N95 masks among residents of Singapore.


title: Re-emergent Human Adenovirus Genome Type 7d Caused an Acute Respiratory Disease Outbreak in Southern China After a Twenty-one Year Absence

text: Human adenoviruses (HAdVs) are highly contagious pathogens causing acute respiratory disease (ARD), among other illnesses. Of the ARD genotypes, HAdV-7 presents with more severe morbidity and higher mortality than the others. We report the isolation and identification of a genome type HAdV-7d (DG01_2011) from a recent outbreak in Southern China. Genome sequencing, phylogenetic analysis, and restriction endonuclease analysis (REA) comparisons with past pathogens indicate HAdV-7d has re-emerged in Southern China after an absence of twenty-one years. Recombination analysis reveals this genome differs from the 1950s-era prototype and vaccine strains by a lateral gene transfer, substituting the coding region for the L1 52/55 kDa DNA packaging protein from HAdV-16. DG01_2011 descends from both a strain circulating in Southwestern China (2010) and a strain from Shaanxi causing a fatality and outbreak (Northwestern China; 2009). Due to the higher morbidity and mortality rates associated with HAdV-7, the surveillance, identification, and characterization of these strains in population-dense China by REA and/or whole genome sequencing are strongly indicated. With these accurate identifications of specific HAdV types and an epidemiological database of regional HAdV pathogens, along with the HAdV genome stability noted across time and space, the development, availability, and deployment of appropriate vaccines are needed.


title: RNA-binding proteins of coronavirus MHV: Detection of monomeric and multimeric N protein with an RNA overlay-protein blot assay

text: Abstract RNA-binding proteins of coronavirus MHV-A59 were identified using an RNA overlay-protein blot assay (ROPBA). The major viral RNA-binding protein in virions and infected cells was the phosphorylated nucleocapsid protein N (50K). A new 140K virus structural protein was identified as a minor RNA-binding protein both in virions and in infected cells. The 140K protein was antigenically related to N, and upon reduction, yielded only 50K N. Thus, the 140K protein is probably a trimer of N subunits linked by intermolecular disulfide bonds. Several cellular RNA-binding proteins were also detected. RNA-binding of N was not nucleotide sequence specific. Single-stranded RNA of MHV, VSV, or cellular origin, a DNA probe of the MHV leader sequence, and double-stranded bovine rotavirus RNA could all bind to N. Binding of MHV RNA was optimal between pH 7 and 8, and the RNA could be eluted in 0.1 M NaCl. The ROPBA is a useful method for the initial identification of RNA-binding proteins, such as N and the 140K protein of murine coronavirus.


title: Parameter estimation and prediction for coronavirus disease outbreak 2019 (COVID-19) in Algeria

text: BACKGROUND: The wave of the coronavirus disease outbreak in 2019 (COVID-19) has spread all over the world. In Algeria, the first case of COVID-19 was reported on 25 February, 2020, and the number of confirmed cases of it has increased day after day. To overcome this difficult period and a catastrophic scenario, a model-based prediction of the possible epidemic peak and size of COVID-19 in Algeria is required. METHODS: We are concerned with a classical epidemic model of susceptible, exposed, infected and removed (SEIR) population dynamics. By using the method of least squares and the best fit curve that minimizes the sum of squared residuals, we estimate the epidemic parameter and the basic reproduction number ℜ(0). Moreover, we discuss the effect of intervention in a certain period by numerical simulation. RESULTS: We find that ℜ(0) = 4.1, which implies that the epidemic in Algeria could occur in a strong way. Moreover, we obtain the following epidemiological insights: the intervention has a positive effect on the time delay of the epidemic peak; the epidemic size is almost the same for a short intervention; a large epidemic can occur even if the intervention is long and sufficiently effective. CONCLUSION: Algeria must implement the strict measures as shown in this study, which could be similar to the one that China has finally adopted.


title: Ethical considerations relevant to infections in pregnancy: application to Covid-19

text: Despite wide diversity and scope, the ethical dimensions relevant to infections in pregnancy remain little explored. Important questions span topics with personal or wider societal and public health impact. The conceptualization of the status and responsibilities of the pregnant woman and the legitimate limits of third-party interests are key determinants of our appreciation of applicable ethical obligations.


title: The p22 RNA silencing suppressor of the crinivirus Tomato chlorosis virus preferentially binds long dsRNAs preventing them from cleavage

text: Abstract Viruses encode silencing suppressor proteins to counteract RNA silencing. Because dsRNA plays a key role in silencing, a general silencing suppressor strategy is dsRNA binding. The p22 suppressor of the plant virus Tomato chlorosis virus (ToCV; genus Crinivirus, family Closteroviridae) has been described as having one of the longest lasting local suppressor activities. However, the mechanism of action of p22 has not been characterized. Here, we show that ToCV p22 binds long dsRNAs in vitro, thus interfering with their processing into small RNAs (sRNAs) by an RNase III-type Dicer homolog enzyme. Additionally, we have studied whether a putative zinc finger motif found in p22 has a role in dsRNA binding and suppressor function. The efficient ability of p22 to suppress RNA silencing, triggered by hairpin transcripts transiently expressed in planta, supports the relationship between its ability to bind dsRNA in vitro and its ability to inhibit RNA silencing in vivo.


title: A Simulation Framework to Investigate in vitro Viral Infection Dynamics

text: Abstract Virus infection is a complex biological phenomenon for which in vitro experiments provide a uniquely concise view where data is often obtained from a single population of cells, under controlled environmental conditions. Nonetheless, data interpretation and real understanding of viral dynamics is still hampered by the sheer complexity of the various intertwined spatio-temporal processes. In this paper we present a tool to address these issues: a cellular automata model describing critical aspects of in vitro viral infections taking into account spatial characteristics of virus spreading within a culture well. The aim of the model is to understand the key mechanisms of SARS-CoV infection dynamics during the first 24hours post infection. We interrogate the model using a Latin Hypercube sensitivity analysis to identify which mechanisms are critical to the observed infection of host cells and the release of measured virus particles.


Better Understanding on MERS Corona Virus Outbreak in Korea


title: Infections in Travelers

text: Travel medicine continues to grow as international tourism and patient medical complexity increases. This article reflects the state of the current field, but new recommendations on immunizations, resistance patterns, and treatment modalities constantly change. The US Centers for Disease Control and the World Health Organization maintain helpful Web sites for both patient and physician. With thoughtful preparation and prevention, risks can be minimized and travel can continue as safely as possible.


title: Determination of mutation trend in proteins by means of translation probability between RNA codes and mutated amino acids

text: Abstract In this study, we estimate the translation probability to amino acid from RNA codon. With the determined 183 translation probabilities and amino-acid composition of eight highly mutated proteins, we construct the theoretical distributions of mutated amino acids in these proteins and then compare them with their actual distributions affected by mutations. Thereafter we trace the pattern of translation probabilities from RNA codons to mutated amino acids of 1053 point missense mutations. Finally, we statistically conclude that the natural mutation trend goes along the theoretical translation probability.


docid: zzvqjfet

title: COVID-19 in pregnant women – Authors' reply


title: Immune response in children with COVID‐19 is characterized by lower levels of T cell activation than infected adults

text: XX XXX This article is protected by copyright. All rights reserved


title: How accurate is self-testing?

text: The UK has embarked on a programme of self-testing for coronavirus, but can swabs taken at home be trusted? Michael Brooks reports


docid: eqbbbibm

title: A case‐controlled study comparing clinical course and outcomes of pregnant and non‐pregnant women with severe acute respiratory syndrome

text: Objective To compare the clinical courses and outcomes of pregnant severe acute respiratory syndrome (SARS) patients and non‐pregnant SARS patients. Design A case–control study. Setting Tertiary Hospital for Infectious Disease. Sample Ten pregnant and 40 non‐pregnant female patients infected with SARS. Methods Clinical course and outcomes of pregnant SARS patients were compared with a group of non‐pregnant SARS patient. Cases and controls were matched with respect to sex, age, timing of contracting SARS, health care workers status and underlying illness. Main outcome measures The incidence of intensive care unit admission, intubation, medical complications and death rate. Results Pregnancy had no discernible impact on clinical symptoms and presentation delay. Four out of the 10 pregnant patients, nevertheless, required endotracheal intubation and six were admitted to the intensive care unit (ICU), as compared with 12.5% intubation rate (P= 0.065) and 17.5% ICU admission rate (P= 0.012) in the non‐pregnant group. More pregnant SARS patients developed renal failure (P= 0.006) and disseminated intravascular coagulopathy (P= 0.006), as compared with non‐pregnant SARS group. There were three deaths in the pregnant group, whereas there was no death in the non‐pregnant control group (P= 0.006). Conclusion Pregnant women with SARS experience a worse clinical course and poorer outcomes compared with non‐pregnant women.


title: Rapid and generic identification of influenza A and other respiratory viruses with mass spectrometry

text: Abstract The rapid identification of existing and emerging respiratory viruses is crucial in combating outbreaks and epidemics. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid and reliable identification method in bacterial diagnostics, but has not been used in virological diagnostics. Mass spectrometry systems have been investigated for the identification of respiratory viruses. However, sample preparation methods were laborious and time-consuming. In this study, a reliable and rapid sample preparation method was developed allowing identification of cultured respiratory viruses. Tenfold serial dilutions of ten cultures influenza A strains, mixed samples of influenza A virus with human metapneumovirus or respiratory syncytial virus, and reconstituted clinical samples were treated with the developed sample preparation method. Subsequently, peptides were subjected to MALDI-TOF MS and liquid chromatography tandem mass spectrometry (LC–MS/MS). The influenza A strains were identified to the subtype level within 3h with MALDI-TOF MS and 6h with LC–MS/MS, excluding the culturing time. The sensitivity of LC–MS/MS was higher compared to MALDI-TOF MS. In addition, LC–MS/MS was able to discriminate between two viruses in mixed samples and was able to identify virus from reconstituted clinical samples. The development of an improved and rapid sample preparation method allowed generic and rapid identification of cultured respiratory viruses by mass spectrometry.


title: Institutions Involved in Food Safety: World Health Organization (WHO)

text: Abstract The World Health Organization (WHO) has been a leading intergovernmental organization in the effort to prevent diseases related to food and improve global food safety and security. These efforts have been focused on the provision of independent scientific advice on foodborne risks, the development of international food standards, through the work of the Food and Agricultural Organization of the United Nations/WHO Codex Alimentarius Commission, and the support of Member States through direct policy advice as well as through the creation of laboratory and authority networks sharing experience and building capacity. WHO has also promoted the development and spread of new policy thinking in the food safety area, including especially the introduction of the new risk analysis paradigm, the holistic, farm-to-fork thinking in relation to food production, now often referred to as ‘One Health,’ and finally the focus on simple and efficient messaging toward preventing food risks through a better understanding of good food preparation practices in all sectors.


docid: mrrctuxt

title: REVIEW: Adult Celiac Disease and the Severe “Flat” Small Bowel Biopsy Lesion

text: Classification of architectural changes in the small intestinal biopsy may be clinically useful to define the cause of diarrhea or suspected malabsorption, especially in adults. Pathologic changes may include severe (flat) or variably severe (mild or moderate) abnormalities. For some disorders, small bowel biopsy findings may be very distinctive and lead to a specific diagnosis. For others, like adult celiac disease, biopsy changes are less specific. Indeed, it is becoming increasingly appreciated that several conditions can produce similar histopathologic changes. Serological assays, including endomysial antibodies and tissue transglutaminase antibodies, may be very useful tools for screening and case finding in clinical practice. However, demonstration of characteristic changes in the small intestinal biopsy is critical, along with a gluten-free diet response.


title: Structural Characterization of the glycoprotein GP2 Core Domain from the CAS Virus, a Novel Arenavirus-like Species

text: Fusion of the viral and host cell membranes is a necessary first step for infection by enveloped viruses, and is mediated by the envelope glycoprotein. The transmembrane subunits from the structurally defined “class I” glycoproteins adopt an α-helical “trimer- of-hairpins” conformation during the fusion pathway. Here we present our studies on the envelope glycoprotein transmembrane subunit, GP2, of the CAS virus (CASV). CASV was recently identified from annulated tree boas (Corallus annulatus) with inclusion body disease and is implicated in the disease etiology. We have generated and characterized two protein constructs consisting of the predicted CASV GP2 core domain. The crystal structure of the CASV GP2 post-fusion conformation indicates a trimeric α-helical bundle that is highly similar to those of Ebola Virus (EBOV) and Marburg Virus (MARV) GP2, despite CASV genome homology to arenaviruses. Denaturation studies demonstrate that the stability of CASV GP2 is pH-dependent with higher stability at lower pH; we propose that this behavior is due to a network of interactions among acidic residues that would destabilize the α-helical bundle under conditions where the side chains are deprotonated. The pH-dependent stability of the post-fusion structure has been observed in EBOV and MARV GP2, as well as other viruses that enter via the endosome. Infection experiments with CASV and the related Golden Gate Virus (GGV) support a mechanism of entry that requires endosomal acidification. Our results suggest that despite being primarily arenavirus-like, the transmembrane subunit of CASV is extremely similar to the filoviruses.


Systemic Viral Infections and Collateral Damage in the Liver


title: Target-shaped combined halo and reversed-halo sign, an atypical chest CT finding in COVID-19

text: Typical chest CT findings in COVID-19 have been described as bilateral peripheral ground glass opacities, with or without consolidation. Halo sign and reversed halo sign have been reported as atypical imaging findings in this disease. However, to the best of our knowledge, combined presence of these signs has never been reported before. Herein, we present a COVID-19 patient with numerous atypical target-shaped, combined halo and reversed halo pulmonary lesions, in the absence of any other underlying disease.


title: Antigenic structure of the E2 glycoprotein from transmissible gastroenteritis coronavirus

text: Abstract The antigenic structure of transmissible gastroenteritis (TGE) virus E2 glycoprotein has been defined at three levels: antigenic sites, antigenic subsites and epitopes. Four antigenic sites (A, B, C and D) were defined by competitive radioimmunoassay (RIA) using monoclonal antibodies (MAbs) selected from 9 fusions. About 20% (197) of the hybridomas specific for TGE virus produced neutralizing MAbs specific for site A, which was one of the antigenically dominant determinants. Site A was differentiated in three antigenic subsites: a, b and c, by characterization of 11 MAb resistant (mar) mutants, that were defined by 8, 3, and 3 MAbs, respectively. These subsites were further subdivided in epitopes. A total of 11 epitopes were defined in E2 glycoprotein, eight of which were critical for virus neutralization. Neutralizing MAbs were obtained only when native virus was used to immunize mice, although to produce hybridomas mice immunizations were made with antigen in the native, denatured, or mixtures of native and denatured form. All neutralizing MAbs reacted to conformational epitopes. The antigenic structure of the E2-glycoprotein has been defined with murine MAbs, but the antigenic sites were relevant in the swine, the natural host of the virus, because porcine sera reacted against these sites. MAbs specific for TGE virus site C reacted to non-immune porcine sera. This reactivity was not directed against porcine immunoglobulins. These results indicated that TGE virus contains epitope(s) also present in some non-immunoglobulin component of porcine serum.


title: COVID‐19‐related anxiety predicts somatic symptoms in the UK population

text: This study aimed to estimate the association between anxiety associated with COVID‐19 and somatic symptoms, using data from a large, representative sample (N = 2,025) of the UK adult population. Results showed that moderate to high levels of anxiety associated with COVID‐19 were significantly associated with general somatic symptoms and in particular with gastrointestinal and fatigue symptoms. This pattern of associations remained significant after controlling for generalized anxiety disorder (GAD), pre‐existing health problems, age, gender, and income. This is the first evidence that anxiety associated with COVID‐19 makes a unique contribution to somatization, above and beyond the effect of GAD.


Rats


title: Distinct genetic clades of enterovirus D68 detected in 2010, 2013, and 2015 in Osaka City, Japan

text: The first upsurge of enterovirus D68 (EV-D68), a causative agent of acute respiratory infections (ARIs), in Japan was reported in Osaka City in 2010. In this study, which began in 2010, we surveyed EV-D68 in children with ARIs and analyzed sequences of EV-D68 strains detected. Real-time PCR of 19 respiratory viruses or subtypes of viruses, including enterovirus, was performed on 2,215 specimens from ARI patients (<10 years of age) collected between November 2010 and December 2015 in Osaka City, Japan. EV-D68 was identified in 18 enterovirus-positive specimens (n = 4 in 2013, n = 1 in 2014, and n = 13 in 2015) by analysis of viral protein 1 (VP1) or VP4 sequences, followed by a BLAST search for similar sequences. All EV-D68 strains were detected between June and October (summer to autumn), except for one strain detected in 2014. A phylogenetic analysis of available VP1 sequences revealed that the Osaka strains detected in 2010, 2013, and 2015 belonged to distinct clusters (Clades C, A, and B [Subclade B3], respectively). Comparison of the 5′ untranslated regions of these viruses showed that Osaka strains in Clades A, B (Subclade B3), and C commonly had deletions at nucleotide positions 681–703 corresponding to the prototype Fermon strain. Clades B and C had deletions from nucleotide positions 713–724. Since the EV-D68 epidemic in 2010, EV-D68 re-emerged in Osaka City, Japan, in 2013 and 2015. Results of this study indicate that distinct clades of EV-D68 contributed to re-emergences of this virus in 2010, 2013, and 2015 in this limited region.


Psychological and Coping Responses to COVID-19 Amongst Residents in Training Across ACGME-I accredited Specialties in Singapore


docid: rlpzejjt

title: The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade

text: Abstract In 2019, a new coronavirus (2019-nCoV) infecting Humans has emerged in Wuhan, China. Its genome has been sequenced and the genomic information promptly released. Despite a high similarity with the genome sequence of SARS-CoV and SARS-like CoVs, we identified a peculiar furin-like cleavage site in the Spike protein of the 2019-nCoV, lacking in the other SARS-like CoVs. In this article, we discuss the possible functional consequences of this cleavage site in the viral cycle, pathogenicity and its potential implication in the development of antivirals.


title: Development of SYBR Green real-time RT-PCR for rapid detection, quantitation and diagnosis of unclassified bovine enteric calicivirus

text: Abstract Unclassified bovine enteric calicivirus (BECV) is a newly recognized bovine enteric calicivirus that differs from bovine norovirus, and which causes diarrhea in the small intestines of calves. To date, methods such as real-time reverse transcription-polymerase chain reaction (RT-PCR) have not been developed for the rapid detection, quantitation and diagnosis of BECV. Presently, a BECV-specific SYBR Green real-time RT-PCR assay was evaluated and optimized. Diarrheic specimens (n =118) collected from 2004 to 2005 were subjected to RT-PCR, nested PCR and SYBR Green real-time RT-PCR. By conventional RT-PCR and nested PCR, 9 (7.6%) and 59 (50%) samples tested positive, respectively, whereas the SYBR Green assay detected BECV in 91 (77.1%) samples. Using BECV RNA standards generated by in vitro transcription, the SYBR Green real-time RT-PCR assay sensitively detected BECV RNA to 1.1×100 copies/μl (correlation coefficiency=0.98). The detection limits of the RT-PCR and nested PCR were 1.1×105 and 1.1×102 copies/μl, respectively. These results indicate that the SYBR Green real-time RT-PCR assay is more sensitive than conventional RT-PCR and nested PCR assays, and has potential as a reliable, reproducible, specific, sensitive and rapid tool for the detection, quantitation and diagnosis of unclassified BECV.


title: How do we teach surgical residents in the COVID-19 era?

text: OBJECTIVE: In response to ongoing concerns regarding transmission of the novel coronavirus (COVID-19), surgical practice has changed for the foreseeable future. Practice guidelines recommend only urgent or emergent surgical procedures be performed to minimize viral transmission. This effectively limits standard training and practice for surgical residents. The purpose of this article is to describe opportunities in surgical simulation, and highlights the challenges associated with training in the COVID-19 era. DESIGN: This is a perspective summarizing the potential role of surgical simulation to target training gaps caused by decreased surgical caseloads. CONCLUSIONS: This manuscript concisely discusses simulation options available to training programs, including the novel concept of “surgical kits.” These kits include all instruments necessary to simulate a procedure at home, effectively pairing safety and utility.


title: A psychoanalytic view of reactions to the coronavirus pandemic in China*

text: The coronavirus pandemic, which apparently began in Wuhan in December 2019, and has persisted to the present day, has had several psychological effects in China. The real danger has produced prolonged stress. Large-group phenomena have been stimulated. Overwhelming affects generated by the real danger have led to regression in the stimulus barrier (or “filter”). The COVID-19 has also triggered unconscious defensive reactions, including obsessional cleaning, counterphobic behavior, humor, and denial. The nationally imposed home quarantine of millions of families has caused in-home conflicts and neurotic repetitions of unresolved childhood issues. Prior psychiatric illnesses have been exacerbated. Health workers, including psychiatrists, psychologists, and psychoanalysts, have experienced emotional depletion. Finally, in families where there has been infection or death, delayed mourning and post-traumatic phenomena have been observed. In each of these situations, different interventions based on psychoanalytic principles have been useful.


title: Astroglia in Sepsis Associated Encephalopathy

text: Cellular pathophysiology of sepsis associated encephalopathy (SAE) remains poorly characterised. Brain pathology in SAE, which is manifested by impaired perception, consciousness and cognition, results from multifactorial events, including high levels of systemic cytokines, microbial components and endotoxins, which all damage the brain barriers, instigate neuroinflammation and cause homeostatic failure. Astrocytes, being the principal homeostatic cells of the central nervous system contribute to the brain defence against infection. Forming multifunctional anatomical barriers, astroglial cells maintain brain-systemic interfaces and restrict the damage to the nervous tissue. Astrocytes detect, produce and integrate inflammatory signals between immune cells and cells of brain parenchyma, thus regulating brain immune response. In SAE astrocytes are present in both reactive and astrogliopathic states; balance between these states define evolution of pathology and neurological outcomes. In humans pathophysiology of SAE is complicated by frequent presence of comorbidities, as well as age-related remodelling of the brain tissue with senescence of astroglia; these confounding factors further impact upon SAE progression and neurological deficits.


title: Waterborne Pathogens: Detection Methods and Challenges

text: Waterborne pathogens and related diseases are a major public health concern worldwide, not only by the morbidity and mortality that they cause, but by the high cost that represents their prevention and treatment. These diseases are directly related to environmental deterioration and pollution. Despite the continued efforts to maintain water safety, waterborne outbreaks are still reported globally. Proper assessment of pathogens on water and water quality monitoring are key factors for decision-making regarding water distribution systems’ infrastructure, the choice of best water treatment and prevention waterborne outbreaks. Powerful, sensitive and reproducible diagnostic tools are developed to monitor pathogen contamination in water and be able to detect not only cultivable pathogens but also to detect the occurrence of viable but non-culturable microorganisms as well as the presence of pathogens on biofilms. Quantitative microbial risk assessment (QMRA) is a helpful tool to evaluate the scenarios for pathogen contamination that involve surveillance, detection methods, analysis and decision-making. This review aims to present a research outlook on waterborne outbreaks that have occurred in recent years. This review also focuses in the main molecular techniques for detection of waterborne pathogens and the use of QMRA approach to protect public health.


title: Clinical characteristics of hospitalized patients with SARS‐CoV‐2 infection: A single arm meta‐analysis

text: OBJECTIVE: We aim to summarize reliable evidence of evidence‐based medicine for the treatment and prevention of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) by analyzing all the published studies on the clinical characteristics of patients with SARS‐CoV‐2. METHODS: PubMed, Cochrane Library, Embase, and other databases were searched. Several studies on the clinical characteristics of SARS‐CoV‐2 infection were collected for meta‐analysis. RESULTS: Ten studies were included in Meta‐analysis, including a total number of 50466 patients with SARS‐CoV‐2 infection. Meta‐analysis shows that, among these patients, the incidence of fever was 0.891 (95% CI: 0.818, 0.945), the incidence of cough was 0.722 (95% CI: 0.657, 0.782), and the incidence of muscle soreness or fatigue was 0.425 (95% CI: 0.213, 0.652). The incidence of acute respiratory distress syndrome (ARDS) was 0.148 (95% CI: 0.046, 0.296), the incidence of abnormal chest computer tomography (CT) was 0.966 (95% CI: 0.921, 0.993), the percentage of severe cases in all infected cases was 0.181 (95% CI: 0.127, 0.243), and the case fatality rate of patients with SARS‐CoV‐2 infection was 0.043 (95% CI: 0.027, 0.061). CONCLUSION: Fever and cough are the most common symptoms in patients with SARS‐CoV‐2 infection, and most of these patients have abnormal chest CT examination. Several people have muscle soreness or fatigue as well as ARDS. Diarrhea, hemoptysis, headache, sore throat, shock, and other symptoms are rare. The case fatality rate of patients with SARS‐CoV‐2 infection is lower than that of Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). This meta‐analysis also has limitations, so the conclusions of this Meta‐analysis still need to be verified by more relevant studies with more careful design, more rigorous execution, and larger sample size.


title: CXCL10/IP-10 in Infectious Diseases Pathogenesis and Potential Therapeutic Implications

text: C-X-C motif chemokine 10 (CXCL10) also known as interferon γ-induced protein 10 kDa (IP-10) or small-inducible cytokine B10 is a cytokine belonging to the CXC chemokine family. CXCL10 binds CXCR3 receptor to induce chemotaxis, apoptosis, cell growth and angiostasis. Alterations in CXCL10 expression levels have been associated with inflammatory diseases including infectious diseases, immune dysfunction and tumor development. CXCL10 is also recognized as a biomarker that predicts severity of various diseases. A review of the emerging role of CXCL10 in pathogenesis of infectious diseases revealed diverse roles of CXCL10 in disease initiation and progression. The potential utilization of CXCL10 as a therapeutic target for infectious diseases is discussed.


title: Spotted Fever Rickettsiosis in a Wildlife Researcher in Sabah, Malaysia: A Case Study

text: We present evidence for a case of spotted fever rickettsiosis with severe complications in a young adult male. Although spotted fever group rickettsiae (SFGR) have been reported as the most prevalent cause of rickettsiosis in rural areas of Sabah, Malaysia since the 1980s, this is the first detailed case report of suspected SFGR in the state. Current data on the prevalence, type, and thorough clinical reports on complications of SFGR and other rickettsioses in Sabah is lacking and required to raise the awareness of such diseases. There is a need to emphasize the screening of rickettsioses to medical personnel and to encourage the use of appropriate antibiotics as early treatment for nonspecific febrile illnesses in this region. Suspected rickettsioses need to be considered as one of the differential diagnoses for patients presenting with acute febrile illness for laboratory investigations, and early treatment instituted.


title: Phages bearing affinity peptides to severe acute respiratory syndromes-associated coronavirus differentiate this virus from other viruses

text: Abstract Background Transmission of SARS-associated coronavirus (SARS-CoV) is now well controlled, nevertheless, it is important to develop effective methods to identify this virus from other pathogens. Objectives The purpose of this study was to identify potential ligands and develop a novel diagnostic test to SARS-CoV using phage display technology. Study design The SARS-CoV spike 1 (S1) protein containing the receptor binding region (RBD) was used as an immobilized target followed by incubation with a 12-mer phage display random peptide library. After four rounds of biopanning, 10 monoclonal phages with specific binding activity to the S1-RBD protein were obtained and subjected to binding and diagnostic assays. Results DNA sequencing showed that two phage displayed peptides HHKTWHPPVMHL (phage-H) and SQWHPRSASYPM (phage-S) that were specific ligands to the S1 protein. Moreover, the selected phage-H and phage-S were capable of differentiating SARS-CoV from other coronaviruses in indirect enzyme-linked immunosorbent assays. Conclusion The peptides identified in this study are useful reagents for detection of SARS-CoV.


title: SARS coronavirus: Unusual lability of the nucleocapsid protein

text: Abstract The severe acute respiratory syndrome (SARS) is a contagious disease that killed hundreds and sickened thousands of people worldwide between November 2002 and July 2003. The nucleocapsid (N) protein of the coronavirus responsible for this disease plays a critical role in viral assembly and maturation and is of particular interest because of its potential as an antiviral target or vaccine candidate. Refolding of SARS N-protein during production and purification showed the presence of two additional protein bands by SDS–PAGE. Mass spectroscopy (MALDI, SELDI, and LC/MS) confirmed that the bands are proteolytic products of N-protein and the cleavage sites are four SR motifs in the serine–arginine-rich region—sites not suggestive of any known protease. Furthermore, results of subsequent testing for contaminating protease(s) were negative: cleavage appears to be due to inherent instability and/or autolysis. The importance of N-protein proteolysis to viral life cycle and thus to possible treatment directions are discussed.


title: Response to COVID‐19 pandemic: Beyond medical education in Brazil

text: We received a response to our Editorial from a group in Brazil that raised valuable concerns about the struggles in transforming medical education in low‐income countries. Here, we address the concerns they raised that reinforce the global need for a "Coalition for Medical Education."


title: Social Distancing in Infection Control: A Lattice Model Demonstration

text: The article illustrates the efficacy of proper social distancing methods during disease outbreaks. We inspect the outbreak by counting the number of ways n individuals are infected, given an initially infected patient introduced in a lattice(c(n)). Using self-avoiding walks on lattices where the infection spreads according to the SIR (Susceptible, Infected, Removed) model, we were able to show an exponential decay of the ratio of initial and final values of c(n) after the distancing methods were employed.


title: Construction, properties, and potential application of infectious plasmids containing Semliki Forest virus full-length cDNA with an inserted intron

text: Abstract Semliki Forest virus (SFV, genus Alphavirus) has a broad host range, high efficiency of viral protein expression, and the ability to stimulate an immune response. These properties have made SFV an attractive tool for development of expression vectors, and plasmid clones containing cDNA of the SFV genome often are used. However, instability of these plasmids resulting from cryptic expression of SFV envelope proteins in Escherichia coli represents a problem both for the development of SFV-based vectors and for SFV research. In this study, an infectious plasmid of SFV, pCMV-SFV4, was constructed; its toxic effect was eliminated by intron insertion in the capsid protein encoding region. When transfected into mammalian cells, the plasmid clone was highly infectious and produced virus with properties identical to those of wild-type SFV. The inserted intron was efficiently and properly removed from the RNA genome of SFV. Therefore, this novel and stabilized infectious SFV plasmid represents a superior tool for basic studies of SFV as well as for biotechnological applications.


title: Genetic variation in the C-type lectin receptor CLEC4M in type 1 von Willebrand Disease patients

text: von Willebrand factor (VWF) levels in healthy individuals and in patients with type 1 von Willebrand disease (VWD) are influenced by genetic variation in several genes, e.g. VWF, ABO, STXBP5 and CLEC4M. This study aims to screen comprehensively for CLEC4M variants and investigate their association with type 1 VWD in the Swedish population. In order to screen for CLEC4M variants, the CLEC4M gene region was re-sequenced and the polymorphic neck region was genotyped in 106 type 1 VWD patients from unrelated type 1 VWD families. Single nucleotide variants (SNV) and variable number tandem repeat (VNTR) allele and genotype frequencies were then compared with 294 individuals from the 1000Genomes project and 436 Swedish control individuals. Re-sequencing identified a total of 42 SNVs. Rare variants showed no accumulation in type 1 VWD patients and are not thought to contribute substantially to type 1 VWD. The only missense mutation (rs2277998, NP_001138379.1:p.Asp224Asn) had a higher frequency in type 1 VWD patients than in controls (4.9%). The VNTR genotypes 57 and 67 were observed at higher frequencies than expected in type 1 VWD patients (6.4% and 6.2%) and showed an increase in patients compared with controls (7.4% and 3.1%). Strong linkage disequilibrium in the CLEC4M region makes it difficult to distinguish between the effect of the missense mutation and the VNTR genotypes. In conclusion, heterozygous VNTR genotypes 57 and 67 of CLEC4M were highly enriched and are the most likely mechanism through which CLEC4M contributes to disease in the Swedish type 1 VWD population.


title: Determination of host RNA helicases activity in viral replication

text: RNA helicases are encoded by all eukaryotic and prokaryotic cells and a minority of viruses. Activity of RNA helicases is necessary for all steps in the expression of cells and viruses and the host innate response to virus infection. Their vast functional repertoire is attributable to the core ATPase-dependent helicase domain in conjunction with flanking domains that are interchangeable and engage viral and cellular cofactors. Here, we address the important issue of host RNA helicases that are necessary for replication of a virus. The chapter covers approaches to identification and characterization of candidate helicases and methods to define the biochemical and biophysical parameters of specificity and functional activity of the enzymes. We discuss the context of cellular RNA helicase activity and virion-associated RNA helicases. The methodology and choice of controls fosters the assessment of the virologic scope of RNA helicases across divergent cell lineages and viral replication cycles.


title: The Urge to Build More Intensive Care Unit Beds and Ventilators: Intuitive but Errant

text: Throughout the COVID-19 crisis, much attention has been devoted to the fraught question of how to allocate intensive care unit beds and mechanical ventilators if the supply of these resources is insufficient to provide them to all patients considered to be in need. The authors believe that the deployment of aggressive medical technology to win the “war” against the pandemic may represent the triumph of deeply human instincts over optimal policy.


title: Beware: Gastrointestinal symptoms can be a manifestation of COVID-19

text: BACKGROUND There is an increasing number of reports on the presentation of gastrointestinal symptoms in cases of COVID-19. AIM To review the studies reporting gastrointestinal symptoms in COVID-19. RESULTS Fifteen articles (2,800 patients) were identified. Gastrointestinal symptom frequency varied from 3.0% to 40.7% and included diarrhea (7.5%), náusea (4.5%), anorexia (4.4%), vomiting (1.3%), abdominal pain (0.5%), and belching/reflux (0.3%). Those symptoms can be the first manifestation of COVID-19, but whether they reflect a better or worse prognosis, is controversial. The potential relation of the angiotensin converting enzyme 2 receptor in the digestive tract as an entry route for the virus is discussed. CONCLUSION Gastrointestinal symptoms may be common in COVID-19, in some cases appearing as the first manifestation, even before fever and respiratory symptoms. Therefore, clinicians and gastroenterologists must be aware of those atypical cases during the current pandemic, as well as of the fecal-oral route and corresponding preventive measures.


title: Developing a hierarchy relation with an expert decision analysis process for selecting the optimal resort type for a Taiwanese international resort park

text: Abstract This study presents a state-of-the-art review of the use of an expert decision analysis process in land-use planning and resort type selection in particular. Additionally, the expert decision analysis process was modified to quantitatively resort types; these assessments involve multiple criteria and interdependent features. This study examines the international resort park type selection in Taiwan.


title: Back to the future: recombinant polyclonal antibody therapeutics

text: Antibody therapeutics are one of the fastest growing classes of pharmaceuticals, with an annual US market over $20 billion, developed to treat a variety of diseases including cancer, auto-immune and infectious diseases. Most are currently administered as a single molecule to treat a single disease, however there is mounting evidence that cocktails of multiple antibodies, each with a unique binding specificity and protective mechanism, may improve clinical efficacy. Here, we review progress in the development of oligoclonal combinations of antibodies to treat disease, focusing on identification of synergistic antibodies. We then discuss the application of modern antibody engineering technologies to produce highly potent antibody preparations, including oligoclonal antibody cocktails and truly recombinant polyclonal antibodies. Specific examples illustrating the synergy conferred by multiple antibodies will be provided for diseases caused by botulinum toxin, cancer and immune thrombocytopenia. The bioprocessing and regulatory options for these preparations will be discussed.


title: Intragastric administration of Lactobacillus casei expressing transmissible gastroentritis coronavirus spike glycoprotein induced specific antibody production

text: Lactobacillus casei strain Shirota was selected as a bacterial carrier for the development of live mucosal vaccines against coronavirus. A 75 kDa fragment of transmissible gastroenteritis coronavirus (TGEV) spike glycoprotein S was used as the model coronavirus antigen. The S glycoprotein was cloned into a Lactobacillus/E. coli shuttle vector (pLP500) where expression and secretion of the glycoprotein S from the recombinant lactobacilli was detected via immunoblotting. Oral immunization of BALB/c mice with recombinant LcS that constitutively expresses the 75 kDa fragment of the glycoprotein S, induced both local mucosal and systemic immune responses against TGEV. Maximum titers of IgG (8.38 ± 0.19 ng/ml of serum) and IgA (64.82 ± 2.9 ng/ml of intestinal water) were attained 32 days post oral inturbation. The induced antibodies demonstrated neutralizing effects on TGEV infection.


title: Scorpion venom components as potential candidates for drug development

text: Abstract Scorpions are well known for their dangerous stings that can result in severe consequences for human beings, including death. Neurotoxins present in their venoms are responsible for their toxicity. Due to their medical relevance, toxins have been the driving force in the scorpion natural compounds research field. On the other hand, for thousands of years, scorpions and their venoms have been applied in traditional medicine, mainly in Asia and Africa. With the remarkable growth in the number of characterized scorpion venom components, several drug candidates have been found with the potential to tackle many of the emerging global medical threats. Scorpions have become a valuable source of biologically active molecules, from novel antibiotics to potential anticancer therapeutics. Other venom components have drawn attention as useful scaffolds for the development of drugs. This review summarizes the most promising candidates for drug development that have been isolated from scorpion venoms.


Low-dose corticosteroid therapy does not delay viral clearance in patients with COVID-1


title: Severe Acute Proximal Pulmonary Embolism and COVID-19: A Word of Caution

text: Abstract Acute pulmonary embolism is an uncharacteristic presentation in patients with COVID-19. Here we describe the case of a young woman presenting with severe pulmonary embolism, without any associated symptoms of infections. A clot in a patent foramen ovale was noted. Despite emergency surgical embolectomy, her clinical conditions continued to deteriorate. She was put on extracorporeal life support and tested positive for COVID-19. She died of multiorgan failure on day 10. COVID-19 may have a thrombogenic effect and it may need to be considered in cases of pulmonary embolism and in absence of any obvious risk factor.


title: Potential for occupational exposures to pathogens during bronchoscopy procedures

text: Bronchoscopy is classified as an aerosol-generating procedure, but it is unclear what drives the elevated infection risk observed among healthcare personnel performing the procedure. The objective of this study was to characterize pathways through which bronchoscopists may be exposed to infectious agents during bronchoscopy procedures. Aerosol number concentrations (0.2–1 µm aerodynamic diameter) were measured using a P-Trak Ultrafine Particle Counter 8525 and mass concentrations (<10 µm) were measured using a SidePak Personal Aerosol Monitor AM510 near the head of patients during bronchoscopy procedures. Procedure pathway, number of patient coughs, number of suctioning events, number of contacts with different surfaces by the pulmonologist, and the use and doffing of personal protective equipment were recorded by the investigator on a specially designed form. Any pulmonologist performing a bronchoscopy procedure was eligible to participate. A total of 18 procedures were observed. Mean particle number and mass concentrations were not elevated during procedures relative to those measured before or after the procedure, on average, but the concentrations were highly variable, exhibiting high levels periodically. Patients frequently coughed during procedures (median 65 coughs, range: 0–565 coughs), and suctioning was commonly performed (median 6.5 suctioning events, range: 0–42). In all procedures, pulmonologists contacted the patient (mean 22.3 contacts, range: 1–48), bronchoscope (mean 19.4 contacts, range: 1–46), and at least one environmental surface (mean 31.2 contacts, range: 3–62). In the majority of procedures, the participant contacted his or her body or personal protective equipment (PPE), with a mean of 17.3 contacts (range: 4–48). More often than not, the observed PPE doffing practices differed from those recommended. Bronchoscopy procedures were associated with short-term increased ultrafine or respirable aerosol concentrations, and there were opportunities for contact transmission.


title: Accelerating supply chains with Ant Colony Optimization across a range of hardware solutions

text: Ant Colony algorithm has been applied to various optimisation problems, however, most of the previous work on scaling and parallelism focuses on Travelling Salesman Problems (TSPs). Although useful for benchmarks and new idea comparison, the algorithmic dynamics do not always transfer to complex real-life problems, where additional meta-data is required during solution construction. This paper explores how the benchmark performance differs from real-world problems in the context of Ant Colony Optimization (ACO) and demonstrate that in order to generalise the findings, the algorithms have to be tested on both standard benchmarks and real-world applications. ACO and its scaling dynamics with two parallel ACO architectures – Independent Ant Colonies (IAC) and Parallel Ants (PA). Results showed that PA was able to reach a higher solution quality in fewer iterations as the number of parallel instances increased. Furthermore, speed performance was measured across three different hardware solutions – 16 core CPU, 68 core Xeon Phi and up to 4 Geforce GPUs. State of the art, ACO vectorisation techniques such as SS-Roulette were implemented using C++ and CUDA. Although excellent for routing simple TSPs, it was concluded that for complex real-world supply chain routing GPUs are not suitable due to meta-data access footprint required. Thus, our work demonstrates that the standard benchmarks are not suitable for generalised conclusions.


docid: vnnnevrl

title: Thrombocytopenia is associated with severe coronavirus disease 2019 (COVID-19) infections: A meta-analysis

text: BACKGROUND: Coronavirus disease 2019 (COVID-19) is a novel infectious disease with lack of established laboratory markers available to evaluate illness severity. In this study, we investigate whether platelet count could differentiate between COVID-19 patients with or without severe disease. Additionally, we evaluate if thrombocytopenia is associated with severe COVID-19. METHODS: An electronic search in Medline, Scopus and Web of Science was performed to identify studies reporting data on platelet count in COVID-19 patients. A meta-analysis was performed, with calculation of weighted mean difference (WMD) of platelet number in COVID-19 patients with or without severe disease and odds ratio (OR) of thrombocytopenia for severe form of COVID-19. RESULTS: Nine studies with 1779 COVID-19 patients, 399 (22.4%) with severe disease, were included in the meta-analysis. The pooled analysis revealed that platelet count was significantly lower in patients with more severe COVID-19 (WMD -31×10(9)/L; 95% CI, from -35 to -29×10(9)/L). A subgroup analysis comparing patients by survival, found an even lower platelet count was observed with mortality (WMD, -48×10(9)/L; 95% CI, -57 to -39×10(9)/L. In the four studies (n=1427) which reported data on rate of thrombocytopenia, a low platelet count was associated with over fivefold enhanced risk of severe COVID-19 (OR, 5.1; 95% CI, 1.8-14.6). CONCLUSIONS: Low platelet count is associated with increased risk of severe disease and mortality in patients with COVID-19, and thus should serve as clinical indicator of worsening illness during hospitalization.


title: Repeated avian infectious bronchitis virus infections within a single chicken farm

text: Genotyping of avian infectious bronchitis virus (IBV) was performed on trachea and kidney samples of six chickens obtained from a single farm in Japan. Using two primer sets targeting the spike (S) protein gene, the S1 and S2 regions of DNA fragments were amplified. Sequences of amplified S1 fragments extracted from both organs were identical among the six chickens, showing a JP-I genotype. Sequences of amplified S2 fragments differed between trachea and kidney samples. The kidney profile showed a group IV genotype, whereas the trachea profile showed an unclassified group. This result showed that two different IBVs infected the six chickens. The first IBV infection induced poor protective immunity in this farm, permitting a second IBV infection to occur.


Advancing Priority Research on the Middle East Respiratory Syndrome Coronavirus


title: Prokaryotic expression of antibodies and affibodies

text: Abstract Recent advances have been made in the development of systems for the display and expression of recombinant antibodies and affibodies in filamentous phages, Escherichia coli and other prokaryotic cells. Emphasis has been placed on improving phage and phagemid vectors, alternative systems for expression in different cellular compartments (e.g. the outer membrane, periplasm, cytoplasm and extracellular secretion) and novel multimerization systems for generating bivalent or multivalent binding molecules.


docid: xjzhilgm

title: COVID-19 diagnostic approaches: different roads to the same destination

text: “SARS-CoV2”, a previously unknown strain of coronaviruses caused a severe respiratory disease called Coronavirus disease (COVID-19) which emerged from Wuhan city of China on 30 December 2019, and declared as Global health problem by World Health Organisation within a month. In less than two and half months (11 March, 2020) it was declared as a pandemic disease due to its rapid spreading ability, it covered more than 211 countries infecting around 1.7 million persons and claiming around 1.1 lakhs lives within merely 100 days of its emergence. Containment of the infection of this virus is the only available measure to control the disease as no vaccine or specific antiviral treatment is available. Confirmed detection of the virus followed by isolation of the infected person at the earliest possible is the only measure to prevent this disease. Although there are number of methods available for detection of virus and to combat this disease in the present pandemic situation, but these available diagnostic methods have their own limitations. The speedy and exponential global spread of this disease strongly urges the fast and economic diagnostics tools. Additional to the available diagnostic methods, there is a sudden surge for development of various of methods and platforms to diagnose the COVID-19. The review summarized the advantage and disadvantage of various diagnostic approaches being used presently for COVID-19, newer detection methods in developmental stage and the feasibility of advanced platforms like newer nano-sensor based on-the-spot detection technologies.


title: SARS-CoV-2-mediated inflammatory response in lungs: should we look at RAGE?

text: The novel coronavirus disease (COVID-19) pandemic is placing significant strains on health systems, scientific communities, essential public services, and economies all over the world. In this context, the world´s scientific biomedical establishment is unleashing an unprecedented response to the COVID-19 pandemic. This is a battle against time, considering the thousands of human lives are lost every day. In this commentary, based on a very recent research report, we intend to highlight how a new mechanism describing the RAGE transactivation produced by Ang II-mediated ATR1 activation can run continuously and thus, reinforcing a sustained inflammation in lungs, due to the SARS-Cov-2-mediated imbalance of the ACE/And II/ATR1 pathway.


title: IFITM Proteins Inhibit Entry Driven by the MERS-Coronavirus Spike Protein: Evidence for Cholesterol-Independent Mechanisms

text: The interferon-inducible transmembrane (IFITM) proteins 1, 2 and 3 inhibit the host cell entry of several enveloped viruses, potentially by promoting the accumulation of cholesterol in endosomal compartments. IFITM3 is essential for control of influenza virus infection in mice and humans. In contrast, the role of IFITM proteins in coronavirus infection is less well defined. Employing a retroviral vector system for analysis of coronavirus entry, we investigated the susceptibility of human-adapted and emerging coronaviruses to inhibition by IFITM proteins. We found that entry of the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV) is sensitive to inhibition by IFITM proteins. In 293T cells, IFITM-mediated inhibition of cellular entry of the emerging MERS- and SARS-CoV was less efficient than blockade of entry of the globally circulating human coronaviruses 229E and NL63. Similar differences were not observed in A549 cells, suggesting that cellular context and/or IFITM expression levels can impact inhibition efficiency. The differential IFITM-sensitivity of coronaviruses observed in 293T cells afforded the opportunity to investigate whether efficiency of entry inhibition by IFITMs and endosomal cholesterol accumulation correlate. No such correlation was observed. Furthermore, entry mediated by the influenza virus hemagglutinin was robustly inhibited by IFITM3 but was insensitive to accumulation of endosomal cholesterol, indicating that modulation of cholesterol synthesis/transport did not account for the antiviral activity of IFITM3. Collectively, these results show that the emerging MERS-CoV is a target of the antiviral activity of IFITM proteins and demonstrate that mechanisms other than accumulation of endosomal cholesterol can contribute to viral entry inhibition by IFITMs.


title: Saikosaponin C exerts anti-HBV effects by attenuating HNF1α and HNF4α expression to suppress HBV pgRNA synthesis

text: OBJECTIVE: Saikosaponin c (SSc), a compound purified from the traditional Chinese herb of Radix Bupleuri was previously identified to exhibit anti-HBV replication activity. However, the mechanism through which SSc acts against HBV remains unknown. In this study, we investigated the mechanism of SSc mediated anti-HBV activity. METHODS: HepG2.2.15 cells were cultured at 37 ℃ in the presence of 1–40 μg/mL of SSc or DMSO as a control. The expression profile of HBV markers, cytokines, HNF1α and HNF4α were investigated by real-time quantitative PCR, Elisa, Western blot and Dot blotting. Knockdown of HNF1α or HNF4α in HepG2.2.15 cells was mediated by two small siRNAs specifically targeting HNF1α or HNF4α. RESULTS: We found that SSc stimulates IL-6 expression, leading to attenuated HNF1α and HNF4α expression, which further mediates suppression of HBV pgRNA synthesis. Knockdown of HNF1α or HNF4α in HepG2.2.15 cells by RNA interference abrogates SSc’s anti-HBV role. Moreover, SSc is effective to both wild-type and drug-resistant HBV mutants. CONCLUSION: SSc inhibits pgRNA synthesis by targeting HNF1α and HNF4α. These results indicate that SSc acts as a promising compound for modulating pgRNA transcription in the therapeutic strategies against HBV infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00011-019-01284-2) contains supplementary material, which is available to authorized users.


title: Review of Artificial Intelligence Techniques in Imaging Data Acquisition, Segmentation and Diagnosis for COVID-19

text: (This paper was submitted as an invited paper to IEEE Reviews in Biomedical Engineering on April 6, 2020.) The pandemic of coronavirus disease 2019 (COVID-19) is spreading all over the world. Medical imaging such as X-ray and computed tomography (CT) plays an essential role in the global fight against COVID-19, whereas the recently emerging artificial intelligence (AI) technologies further strengthen the power of the imaging tools and help medical specialists. We hereby review the rapid responses in the community of medical imaging (empowered by AI) toward COVID-19. For example, AI-empowered image acquisition can significantly help automate the scanning procedure and also reshape the workflow with minimal contact to patients, providing the best protection to the imaging technicians. Also, AI can improve work efficiency by accurate delination of infections in X-ray and CT images, facilitating subsequent quantification. Moreover, the computer-aided platforms help radiologists make clinical decisions, i.e., for disease diagnosis, tracking, and prognosis. In this review paper, we thus cover the entire pipeline of medical imaging and analysis techniques involved with COVID-19, including image acquisition, segmentation, diagnosis, and follow-up. We particularly focus on the integration of AI with X-ray and CT, both of which are widely used in the frontline hospitals, in order to depict the latest progress of medical imaging and radiology fighting against COVID-19.


title: Enteric viruses in Brazilian turkey flocks: Single and multiple virus infection frequency according to age and clinical signs of intestinal disease

text: Poult enteritis complex has been associated with enteritis and reduction in growth rates in commercial turkeys worldwide. Intestinal samples from 76 turkey flocks from different Brazilian states affected or not with intestinal disorders were evaluated for the presence of adenovirus groups 1 and 2 (TAV), astrovirus types 1 and 2 (TAstV-1 and TAstV-2), turkey coronavirus (TCoV), reovirus, rotavirus, and avian nephritis virus (ANV) using PCR. The percentage of positive samples was categorized according to the geographic origin, age of the flocks, and presence of clinical signs of intestinal disease. The percentage of samples that were positive for at least one virus was 93.4%, whereas the percentage of samples that were positive for more than one virus was 69.7%. An average of 3.20 viruses per sample was detected in turkeys in the growing phase of the production cycle (1 to 4 wk of age). The TAstV-1 and TCoV were the most frequently observed viruses in growing phase turkeys and occurred simultaneously in 85% of these samples. In turkeys in the finishing phase of development (5 to 18 wk), a lower average number of viruses was observed (2.41), and the most frequent viruses isolated in these turkeys were TAstV-1 (57.1%) and rotavirus (51.8%). Overall, every virus was detected more frequently in growing phase turkeys than in finishing phase turkeys with the exception of TAV. Samples from flocks exhibiting clinical signs of intestinal disease showed a higher rate of positivity, and TAstV-1, TAstV-2, and TCoV were the most frequently occurring viruses in this cohort. Birds without clinical signs most frequently harbored TAstV-1 and rotavirus. Future studies should focus on the description and elucidation of the role of each virus, as well as the pathogenic and immunological implications of the different combinations of viruses in turkeys.


title: Autophagy, antiviral immunity, and viral countermeasures

text: The autophagy pathway likely evolved not only to maintain cellular and tissue homeostasis but also to protect cells against microbial attack. This conserved mechanism by which cytoplasmic cargo is delivered to the endolysosomal system is now recognized as a central player in coordinating the host response to diverse intracellular pathogens, including viruses. As an endolysosomal delivery system, autophagy functions in the transfer of viruses from the cytoplasm to the lysosome where they are degraded, in the transfer of viral nucleic acids to endosomal sensors for the activation of innate immunity, and in the transfer of endogenous viral antigens to MHC class II compartments for the activation of adaptive immunity. Viruses have, in turn, evolved different strategies to antagonize, and potentially, to exploit the host autophagic machinery. Moreover, through mechanisms not yet well understood, autophagy may dampen host innate immune and inflammatory responses to viral infection. This review highlights the roles of autophagy in antiviral immunity, viral strategies to evade autophagy, and potential negative feedback functions of autophagy in the host antiviral response.


title: Inhibition of a Putative Dihydropyrimidinase from Pseudomonas aeruginosa PAO1 by Flavonoids and Substrates of Cyclic Amidohydrolases

text: Dihydropyrimidinase is a member of the cyclic amidohydrolase family, which also includes allantoinase, dihydroorotase, hydantoinase, and imidase. These metalloenzymes possess very similar active sites and may use a similar mechanism for catalysis. However, whether the substrates and inhibitors of other cyclic amidohydrolases can inhibit dihydropyrimidinase remains unclear. This study investigated the inhibition of dihydropyrimidinase by flavonoids and substrates of other cyclic amidohydrolases. Allantoin, dihydroorotate, 5-hydantoin acetic acid, acetohydroxamate, orotic acid, and 3-amino-1,2,4-triazole could slightly inhibit dihydropyrimidinase, and the IC(50) values of these compounds were within the millimolar range. The inhibition of dihydropyrimidinase by flavonoids, such as myricetin, quercetin, kaempferol, galangin, dihydromyricetin, and myricitrin, was also investigated. Some of these compounds are known as inhibitors of allantoinase and dihydroorotase. Although the inhibitory effects of these flavonoids on dihydropyrimidinase were substrate-dependent, dihydromyricetin significantly inhibited dihydropyrimidinase with IC(50) values of 48 and 40 μM for the substrates dihydrouracil and 5-propyl-hydantoin, respectively. The results from the Lineweaver−Burk plot indicated that dihydromyricetin was a competitive inhibitor. Results from fluorescence quenching analysis indicated that dihydromyricetin could form a stable complex with dihydropyrimidinase with the K (d) value of 22.6 μM. A structural study using PatchDock showed that dihydromyricetin was docked in the active site pocket of dihydropyrimidinase, which was consistent with the findings from kinetic and fluorescence studies. This study was the first to demonstrate that naturally occurring product dihydromyricetin inhibited dihydropyrimidinase, even more than the substrate analogs (>3 orders of magnitude). These flavonols, particularly myricetin, may serve as drug leads and dirty drugs (for multiple targets) for designing compounds that target several cyclic amidohydrolases.


title: The papain-like protease of avian infectious bronchitis virus has deubiquitinating activity

text: Coronavirus papain-like proteases (PLPs) can act as proteases that process virus-encoded large replicase polyproteins and also as deubiquitinating (DUB) enzymes. Like the PLPs of other coronaviruses (CoVs), the avian infectious bronchitis virus (IBV) PLP catalyzes proteolysis of Gly-Gly dipeptide bonds to release mature cleavage products. However, the other functions of the IBV PLP are not well understood. In this study, we found that IBV exhibits strong global DUB activity with significant reductions of the levels of ubiquitin (Ub)-, K48-, and K63-conjugated proteins. The DUB activity exhibited a clear time dependence, with stronger DUB activity in the early stage of viral infection. Furthermore, the IBV replicase-encoded PLP, including the downstream transmembrane (TM) domain, is a DUB enzyme and dramatically reduced the level of Ub-conjugated proteins, while processing both K48- and K63-linked polyubiquitin chains. By contrast, PLP did not cause any reduction of haemagglutinin (HA)-Ub-conjugated proteins. In addition, mutations of the catalytic residues of PLP-TM, Cys1274Ser and His1437Lys, reduced DUB activity against Ub-, K48- and K63- conjugated proteins, indicating that the DUB activity of the PLP-TM wild-type protein is not completely dependent on its catalytic activity. Overall, these results demonstrate that the IBV-encoded PLP-TM functions as a DUB enzyme and suggest that IBV may interfere with the activation of host antiviral signaling pathway by degrading polyubiquitin-associated proteins.


Ventilation of COVID-19 patients in intensive care units