title: Finding comfort in nature

text: The global coronavirus crisis may redefine our relationship to the natural world. In times of apocalyptic news from many countries affected by COVID-19, news stories of conservation successes, receding pollution and wild animals exploring deserted cities appear as silver linings. The widely shared experience of vulnerability may even shock humanity into addressing those other global risks that were never taken seriously enough, including climate change and antibiotics resistance. Michael Gross reports.


title: A community-based approach to influenza assessment and treatment during a pandemic

text: Abstract In the event of an influenza pandemic, hospitals and community-based health services will be overwhelmed. To ensure that life-saving health services are able to continue, the Ontario Health Plan for an Influenza Pandemic (OHPIP) provides direction for assessing and treating patients with influenza, remotely and through the implementation of alternate assessment, treatment and referral centres (Flu Centres). The OHPIP also provides tools and resources for local pandemic planners to assist them with the implementation of this strategy.


title: Middle East Respiratory Syndrome Infection Control and Prevention Guideline for Healthcare Facilities

text: Middle East Respiratory Syndrome (MERS) is an acute viral respiratory illness with high mortality caused by a new strain of betacoronavirus (MERS-CoV). Since the report of the first patient in Saudi Arabia in 2012, large-scale outbreaks through hospital-acquired infection and inter-hospital transmission have been reported. Most of the patients reported in South Korea were also infected in hospital settings. Therefore, to eliminate the spread of MERS-CoV, infection prevention and control measures should be implemented with rigor. The present guideline has been drafted on the basis of the experiences of infection control in the South Korean hospitals involved in the recent MERS outbreak and on domestic and international infection prevention and control guidelines. To ensure efficient MERS-CoV infection prevention and control, care should be taken to provide comprehensive infection control measures including contact control, hand hygiene, personal protective equipment, disinfection, and environmental cleaning.


title: Future Perspectives on Infections Associated with Gastrointestinal Tract Diseases

text: There are a vast number of infectious agents that are associated with gastrointestinal (GI) tract diseases. The epidemiology of GI diseases is changing, with a greater number of conditions increasing in incidence. Challenges exist with establishing cause-and-effect relationships because of the ubiquitous nature of these organisms and the milieu in which they exist. Advances in technology should provide novel methods for identifying and diagnosing these organisms and the relationship they have with a specific digestive disease.


title: Coronavirus N protein N-terminal domain (NTD) specifically binds the transcriptional regulatory sequence (TRS) and melts TRS-cTRS RNA duplexes

text: All coronaviruses (CoVs), including the causative agent of severe acute respiratory syndrome (SARS), encode a nucleocapsid (N) protein that harbors two independent RNA binding domains of known structure, but poorly characterized RNA binding properties. We show here that the N-terminal domain (NTD) of N protein from mouse hepatitis virus (MHV), a virus most closely related to SARS-CoV, employs aromatic amino acid-nucleobase stacking interactions with a triple adenosine motif to mediate high-affinity binding to single-stranded RNAs containing the transcriptional regulatory sequence (TRS) or its complement (cTRS). Stoichiometric NTD fully unwinds a TRS-cTRS duplex that mimics a transiently formed transcription intermediate in viral subgenomic RNA synthesis. Mutation of the solvent-exposed Y127, positioned on the β-platform surface of our 1.75 Å structure, binds the TRS far less tightly and is severely crippled in its RNA unwinding activity. In contrast, the C-terminal domain (CTD) exhibits no RNA unwinding activity. Viruses harboring Y127A N mutation are strongly selected against and Y127A N does not support an accessory function in MHV replication. We propose that the helix melting activity of the coronavirus N protein NTD plays a critical accessory role in subgenomic RNA synthesis and other processes requiring RNA remodeling.


title: A new nidovirus (NamDinh virus NDiV): Its ultrastructural characterization in the C6/36 mosquito cell line

text: Abstract We describe the ultrastructure of the NamDinh virus (NDiV), a new member of the order Nidovirales grown in the C6/36 mosquito cell line. Uninfected and NDiV-infected cells were investigated by electron microscopy 24–48h after infection. The results show that the viral nucleocapsid-like particles form clusters concentrated in the vacuoles, the endoplasmic reticulum, and are scattered in the cytoplasm. Mature virions of NDiV were released as budding particles on the cell surface where viral components appear to lie beneath and along the plasma membrane. Free homogeneous virus particles were obtained by ultracentrifugation on sucrose gradients of culture fluids. The size of the round-shaped particles with a complete internal structure was 80nm in diameter. This is the first study to provide information on the morphogenesis and ultrastructure of the first insect nidovirus NDiV, a missing evolutionary link in the emergence of the viruses with the largest RNA genomes.


Addressing the shortage of personal protective equipment during the COVID-19 pandemic in India-A public health perspective


title: Diseases at the livestock–wildlife interface: Status, challenges, and opportunities in the United States

text: Abstract In the last half century, significant attention has been given to animal diseases; however, our understanding of disease processes and how to manage them at the livestock–wildlife interface remains limited. In this study, we conduct a systematic review of the scientific literature to evaluate the status of diseases at the livestock–wildlife interface in the United States. Specifically, the goals of the literature review were three fold: first to evaluate domestic animal diseases currently found in the United States where wildlife may play a role; second to identify critical issues faced in managing these diseases at the livestock–wildlife interface; and third to identify potential technical and policy strategies for addressing these issues. We found that of the 86 avian, ruminant, swine, poultry, and lagomorph diseases that are reportable to the World Organization for Animal Health (OIE), 53 are present in the United States; 42 (79%) of these have a putative wildlife component associated with the transmission, maintenance, or life cycle of the pathogen; and 21 (40%) are known to be zoonotic. At least six of these reportable diseases—bovine tuberculosis, paratuberculosis, brucellosis, avian influenza, rabies, and cattle fever tick (vector control)—have a wildlife reservoir that is a recognized impediment to eradication in domestic populations. The complex nature of these systems highlights the need to understand the role of wildlife in the epidemiology, transmission, and maintenance of infectious diseases of livestock. Successful management or eradication of these diseases will require the development of cross-discipline and institutional collaborations. Despite social and policy challenges, there remain opportunities to develop new collaborations and new technologies to mitigate the risks posed at the livestock–wildlife interface.


title: Human Infection with MERS Coronavirus after Exposure to Infected Camels, Saudi Arabia, 2013

text: We investigated a case of human infection with Middle East respiratory syndrome coronavirus (MERS-CoV) after exposure to infected camels. Analysis of the whole human-derived virus and 15% of the camel-derived virus sequence yielded nucleotide polymorphism signatures suggestive of cross-species transmission. Camels may act as a direct source of human MERS-CoV infection.


COVID-19 and Smoking


title: The emergence of porcine epidemic diarrhoea in Croatia: molecular characterization and serology

text: BACKGROUND: Porcine epidemic diarrhoea (PED) is an emergent/re-emergent viral pig disease (caused by the virus belonging to the Coronaviridae family, in specific the Alphacoronavirus genus) of global importance. Clinical presentation is characterized with acute diarrhoea, vomiting and dehydration in pigs of all ages, with a possible high mortality in suckling piglets. The disease emerged in the USA in 2013 causing heavy losses, and re-emerged in Europe in 2014, but with milder consequences. RESULTS: In the spring 2016, PED-like symptoms were reported to be seen on an agricultural holding in Eastern Croatia; laboratory workup confirmed the Croatia’s first PED outbreak ever. Porcine epidemic diarrhoea virus (PEDV) strain responsible for the outbreak was of the S-INDEL genotype, much the same as other European PEDV strains. In 2017, a post-outbreak serology was carried out in three counties in Eastern Croatia, revealing seropositivity in pigs bred on four large industrial holdings (9.09%). The seroprevalence across PEDV-positive holdings was up to 82.8%. The latter holdings were unanimously managed by an enterprise that had never reported PED before. CONCLUSIONS: PED has emerged in Croatian pig population causing potentially considerable losses. The circulating strain was of the S-INDEL genotype. Serological workup proved PEDV spread to another four agricultural holdings, demonstrating the importance of not only external, but also internal biosecurity measures.


title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS

text: Abstract The SARS-CoV spike glycoprotein (S) is the main target of the protective immune response in humans and animal models of SARS. Here, we demonstrated that efficient expression of S from the wild-type spike gene in cultured cells required the use of improved plasmid vectors containing donor and acceptor splice sites, as well as heterologous viral RNA export elements, such as the CTE of Mazon-Pfizer monkey virus or the PRE of Woodchuck hepatitis virus (WPRE). The presence of both splice sites and WPRE markedly improved the immunogenicity of S-based DNA vaccines against SARS. Upon immunization of mice with low doses (2 μg) of naked DNA, only intron and WPRE-containing vectors could induce neutralizing anti-S antibodies and provide protection against challenge with SARS-CoV. Our observations are likely to be useful for the construction of plasmid and viral vectors designed for optimal expression of intronless genes derived from cytoplasmic RNA viruses.


title: ATENCION PRIMARIA Y RESIDENCIAS DE ANCIANOS: A PROPOSITO DE LA COVID-19

text: Resumen Las residencias de ancianos han sido especialmente golpeadas durante la crisis por la actual pandemia por COVID-19. En el momento de redactar este artículo son más de 17.500 los ancianos que fallecieron por coronavirus y que vivían en residencias, más de un 66% de las defunciones. Las tasas de contagio y letalidad en la población institucionalizada son altas por la avanzada edad y deficitario sistema inmune, la presencia de comorbilidades, porque se trata personas frágiles, porque conviven con otros residentes y cuidadores en una institución cerrada y la transmisibilidad es fácil en un contexto de alta contagiosidad y virulencia del virus. Las personas de edad avanzada presentan con mayor frecuencia las formas más graves de la enfermedad. Las presentaciones atípicas son más frecuentes en ancianos y puede retrasar el diagnóstico. La prueba de “Reacción en Cadena de la Polimerasa” (PCR) en los primeros 7 días para la detección de RNA viral del SARS-CoV-2 se considera “Gold standard”. Los criterios de derivación a un centro hospitalario desde los centros residenciales deberían tener en cuenta una valoración de la comorbilidad, la gravedad, la presencia de deterioro cognitivo grave y la dependencia o la necesidad de soporte ventilatorio en pacientes graves. Los centros sociosanitarios deben disponer de planes de contingencia para ofrecer una respuesta ante aparición de casos de COVID-19. El aislamiento durante las pandemias puede tener importantes consecuencias físicas y psicosociales en los residentes. Durante la pandemia del COVID-19 se han puesto en evidencia carencias importantes en el actual modelo residencial. Abstract Rest homes for the elderly have been particularly hit during the crisis due the current COVID-19 pandemic. At the time of writing this article, more than 17,500 elderly people that lived in Care Homes have died due to coronavirus, more than 66% of the deaths. The infection and mortality rates in the institutionalised population are high. This is due to the advanced age, immune system deficit, and the presence of comorbidities, as well as because there are frail, because they live with other residents and carers in a closed institution, and transmission is easy in the context of a highly contagious and virulent virus. The elderly often have more severe forms of the disease. Atypical presentations are more frequent in the elderly and can delay the diagnosis. The Polymer Chain Reaction (PCR) test in the first 7 days for the detection of SARS-CoV-2 viral RNA is considered the test of reference (“Gold standard”). The criteria for referring to a hospital site from Care Homes should take into account an assessment of comorbidity, the severity, the presence of severe cognitive impairment, and the dependency or necessity of ventilatory support in seriously ill patients. The social-health centres should have contingency plans available in order to offer a response when cases of COVID-19 appear. Isolation during pandemics may have important physical and psychosocial consequences in the residents. During the COVID-19 pandemic it has been shown that there have been significant failures in the current care home model.


title: Migration of encephalitogenic CD8 T cells into the central nervous system is dependent on the α4β1‐integrin

text: Although CD8 T cells are key players in neuroinflammation, little is known about their trafficking cues into the central nervous system (CNS). We used a murine model of CNS autoimmunity to define the molecules involved in cytotoxic CD8 T‐cell migration into the CNS. Using a panel of mAbs, we here show that the α4β1‐integrin is essential for CD8 T‐cell interaction with CNS endothelium. We also investigated which α4β1‐integrin ligands expressed by endothelial cells are implicated. The blockade of VCAM‐1 did not protect against autoimmune encephalomyelitis, and only partly decreased the CD8(+) T‐cell infiltration into the CNS. In addition, inhibition of junctional adhesion molecule‐B expressed by CNS endothelial cells also decreases CD8 T‐cell infiltration. CD8 T cells may use additional and possibly unidentified adhesion molecules to gain access to the CNS.


title: Quantitative comparison of the efficiency of antibodies against S1 and S2 subunit of SARS coronavirus spike protein in virus neutralization and blocking of receptor binding: Implications for the functional roles of S2 subunit()

text: Neutralizing effects of antibodies targeting the C-terminal stalk (S2) subunit of the spike protein of severe acute respiratory syndrome coronavirus have previously been reported, although its mechanism remained elusive. In this study, high titered mouse antisera against the N-terminal globular (S1) and S2 subunits of the S protein were generated and total immunoglobulin G (IgG) was purified from these antisera. The efficiency of these purified IgGs in virus neutralization and blocking of receptor binding were compared quantitatively using virus neutralization assay and a previously developed cell-based receptor binding assay, respectively. We demonstrated that anti-S1 IgG neutralizes the virus and binds to the membrane associated S protein more efficiently than anti-S2 IgG does. Moreover, both anti-S1 and anti-S2 IgGs were able to abolish the binding between S protein and its cellular receptor(s), although anti-S1 IgG showed a significantly higher blocking efficiency. The unexpected blocking ability of anti-S2 IgG towards the receptor binding implied a possible role of the S2 subunit in virus docking process and argues against the current hypothesis of viral entry. On the other hand, the functional roles of the previously reported neutralizing epitopes within S2 subunit were investigated using an antigen specific antibody depletion assay. Depletion of antibodies against these regions significantly diminished, though not completely abolished, the neutralizing effects of anti-S2 IgG. It suggests the absence of a major neutralizing domain on S2 protein. The possible ways of anti-S2 IgGs to abolish the receptor binding and the factors restricting anti-S2 IgGs to neutralize the virus are discussed.


title: Virus and cystic fibrosis: Rhinoviruses are associated with exacerbations in adult patients

text: Abstract Background Few studies have suggested the potential role of respiratory viruses in cystic fibrosis (CF) exacerbation, but their real impact is probably underestimated. Method Sixty-four sputum samples collected from 46 adult patients were included in the study: 33 samples were collected during exacerbation of CF, and 31 during the stable phase. After extraction, nucleic acids were tested for the presence of respiratory viruses. When rhinovirus (HRV) was detected, the 5′UTR and VP4/2 regions were sequenced, and phylogenetically analyzed. The characteristics of patients in exacerbation and stable phase were compared. Results Viruses were found in 25% of samples. The HRV viruses were the most frequently detected followed by coronaviruses. Only the HRV detection was significantly associated with the occurrence of CF pulmonary exacerbation (p <0.027). Characterization of 5′UTR and VP4/2 regions of the HRV genome specified that HRV-A, -B, -C were detected. All HRV-C were recombinant HRV-Ca. Conclusions HRV were the most frequently detected viruses; their detection was significantly associated with the occurrence of an exacerbation. The reality of viral recombination between HRV was demonstrated in CF patients for the first time, raising the role of viruses in lung microbiota. Further studies are now warranted to decipher virus impact in CF.


title: Multiple assays in a real-time RT-PCR SARS-CoV-2 panel can mitigate the risk of loss of sensitivity by new genomic variants during the COVID-19 outbreak

text: Abstract Objectives In this study, five SARS-CoV-2 PCR assay panels were evaluated against the accumulated genetic variability of the virus to assess the effect on sensitivity of the individual assays. Design or methods As of week 21, 2020, the complete set of available SARS-CoV-2 genomes from GISAID and GenBank databases were used in this study. SARS-CoV-2 primer sequences from publicly available panels (WHO, CDC, NMDC, and HKU) and QIAstat-Dx were included in the alignment, and accumulated genetic variability affecting any oligonucleotide annealing was annotated. Results A total of 11,627 (34.38%) genomes included single mutations affecting annealing of any PCR assay. Variations in 8,773 (25.94%) genomes were considered as high risk, whereas additional 2,854 (8.43%) genomes presented low frequent single mutations and were predicted to yield no impact on sensitivity. In case of the QIAstat-Dx SARS-CoV-2 Panel, 99.11% of the genomes matched with a 100% coverage all oligonucleotides, and critical variations were tested in vitro corroborating no loss of sensitivity. Conclusions This analysis stresses the importance of targeting more than one region in the viral genome for SARS-CoV-2 detection to mitigate the risk of loss of sensitivity due to the unknown mutation rate during this SARS-CoV-2 outbreak.INTRODUCTIONSince the beginning of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak in December 2019 (Zhu et al., 2020), the number of confirmed cases has been rising dramatically (The Open Science Prize, 2020). According to data from the World Health Organization (WHO), Coronavirus Disease 2019 or COVID-19 (Gorbalenya et al., 2020) has been diagnosed in over 6,057,853 people from more than 200 countries or territories and caused over 371,166 deaths worldwide as of 1 June 2020 (World Health Organization, 2020a).SARS-CoV-2 is the seventh coronavirus known to infect humans and it appears to have its origin from zoonotic transmission similar to SARS-CoV (2002) and MERS-CoV (2012) (Andersen et al., 2020). SARS-CoV-2 is hypothesised to be the product of recombination or mutation from a genetically related SARS-CoV species hosted by bats (Sun et al., 2020). Unlike seasonal human coronaviruses HKU1, NL63, OC43 and 229E which are associated with mild symptoms (Corman et al., 2018), SARS-CoV-2 can cause pneumonia and severe acute respiratory syndrome (Andersen et al., 2020). All coronaviruses are single, positive-stranded RNA viruses with similar genomic ∼30kb size and structure. These genes encode non-structural proteins (ORF1a and ORF1b) involved in replication at the 5′-end and multiple structural proteins (spike (S), envelope (E), membrane (M) and nucleocapsid (N)) downstream that make up the virus particle (Chan et al., 2020; Wu et al., 2020).During novel RNA viral outbreaks, detection of the virus relies on real-time reverse transcription polymerase chain reaction (real-time RT-PCR) for detection of the RNA of the virus In the case of SARS-CoV-2, RT-PCR is used for confirmatory diagnosis of symptomatic patients as well as increasingly screening of asymptomatic contacts and subjects at risk. The unprecedented outbreak posed the challenge of evaluating the different diagnostic RT-PCR assays sensitivity and specificity without a previous established gold standard.Since the availability of the first SARS-CoV-2 genomic sequence (Wu et al., 2020), several studies have reported a rapid genetic evolution of SARS-CoV-2 through a phylogenetic tree tracking the geographical spread of the virus (Andersen et al., 2020; The Open Science Prize, 2020; Wu et al., 2020; Yi, 2020). As previously established for RNA viruses, the nucleotide mutation rate of SARS-CoV-2 is estimated to be 8E-04 substitutions per site per year as a consequence of the lack of proofreading activity of polymerases (Lauring and Andino, 2020; The Open Science Prize, 2020). It evinces that new genetic variations of SARS-CoV-2 that will most likely occur during this evolving outbreak could compromise the sensitivity and specificity of RT-PCR detection (Lippi et al., 2020).Specifically, both natural mutation rate of a virus (Lauring and Andino, 2020) and active viral recombination (Yi, 2020) could potentially impair the efficiency of oligonucleotide annealing (Lippi et al., 2020), affecting sensitivity (increasing the limit of detection) or inclusivity (missed detection of some strains due to genomic changes). We hypothesize that in order to minimize the risk of sensitivity loss of RT-PCR for detecting novel viruses with unknown genetic variability like SARS-CoV-2, published RT-PCR design strategies for SARS-CoV-2 detection should target more than one region in the viral genome. This was the general approach followed to obtain the earliest available SARS-CoV-2 RT-PCR assays in panels used worldwide (Centers for Disease Control and Prevention, 2020a, 2020b; Chu et al., 2020; Corman et al., 2020; National Microbiology Data Center, 2020; QIAstat-Dx Respiratory SARS-CoV-2 Panel, 2020; University of Hong Kong, 2020; World Health Organization, 2020b), including the syndromic multiplex QIAstat-Dx Respiratory SARS-CoV-2 Panel (Table 1). The selected conserved target regions from available SARS-CoV-2 genomes minimizes the potential cross-reactivity with other coronaviruses (Gorbalenya et al., 2020; Zhu et al., 2020), including human coronaviruses (Wu et al., 2020) and bat-SARS-like coronaviruses (Chan et al., 2020).The goal of this study is to assess how the genetic variability observed in the SARS-CoV-2 genome as of week 21, 2020 has affected sensitivity of publicly available SARS-CoV-2 real-time RT-PCR Panel assays. Additionally, a detailed characterization and evaluation of the impact on performance of the SARS-CoV-2 assays in the QIAstat-Dx Respiratory SARS-CoV-2 Panel was carried out.METHODSThe complete set of available SARS-CoV-2 genomes larger than 26,000 nucleotides from GISAID (https://www.gisaid.org/) and GenBank (http://www.ncbi.nlm.nih.gov/genbank/) databases were used in this study. As of week 21, 2020, a total of 30,090 and 3,729 available genomes (GISAID and GenBank respectively, Table S1) were aligned using ClustalW algorithm implemented in Geneious software v.10.0.3. (http://www.geneious.com), with a gap open and extent cost of 5 and 3 respectively. The output alignment was curated manually.SARS-CoV-2 primer sequences from publicly available panels (WHO, CDC, NMDC, and HKU) and QIAstat-Dx (Table 1) were included in the alignment, and accumulated genetic variability affecting any oligonucleotide annealing was annotated (Table S2). Variations were considered as high risk when they were placed in the three last nucleotides of the 3’-end, affecting the PCR elongation step (Stadhouders et al., 2010; Whiley and Sloots, 2005) or in the 5’-end of the probe affecting the natural 5’- exonuclease activity of the polymerases (Smith et al., 2002). In addition, were also considered as high risk those variations with a significant presence (>1%) among all published genomes that could become more extended worldwide in the current or potential future spread episodes.RESULTSResults showed large nucleotide insertions (EPI_ISL_416672, EPI_ISL_418061, EPI_ISL_418066, EPI_ISL_416720, EPI_ISL_423027, EPI_ISL_424274, EPI_ISL_424327, EPI_ISL_426134, EPI_ISL_427267, EPI_ISL_429646, EPI_ISL_430896, EPI_ISL_434554, EPI_ISL_437867, EPI_ISL_445217) or fragment gene inversions (EPI_ISL_427289, EPI_ISL_427291) mainly in the polyprotein Orf1ab gene, typically indicating genetic recombination common in coronavirus genomes (Sun et al., 2020; Yi, 2020). Since none of them were placed in binding regions of any of the PCR assays, recombination analysis was considered out of the scope of this current study.A total of 11,627 (34.38%) genomes included single mutations affecting annealing of any PCR assay. Variations in 8,773 (25.94%) genomes were considered as high risk: a) a trinucleotide variation (GGG to AAC) present in 8,251 of the 8,257 (24.41%) genomes affecting the binding of the N gene NMDC assay forward primer; b) different single variations in the last three positions of the 3’-end or 5’-end (primers and probes respectively)..Genetic variations affecting annealing of more than one oligonucleotide of the same assay were not frequent: a) a total of 126 out of the 128 genomes with a non-critical mismatch in Reverse primer of the WHO RdRp assay (Table 2) present any other variation in the Probe (RdRp_SARSr-P2) or in the Forward primer binding regions, b) 17 out of the 8,251 genomes with multiple three consecutive mismatches at the 5’-end (GGG to AAC) of the NMDC N assay presented additional single variations in the Probe or Reverse primer binding regions; c) five genome sequences (EPI_ISL_444736 for the WHO N assay; EPI_ISL_437536, EPI_ISL_422983 and MT293178 for the CDC N1 assay; and EPI_ISL_446918 for the CDC N2 assay) presented combinations of non-critical mismatches among different oligonucleotides of the same set.Additional 2,854 (8.44%) genomes presented low frequent single mutations considered to be low risk (Table 2) and were predicted to yield no impact on sensitivity. However, the effect in every PCR performance must be evaluated individually based on the corresponding PCR thermal profile conditions. The impact of non-3 terminal mismatches should not be underestimated, especially in a diagnostic environment (Stadhouders et al., 2010; Whiley and Sloots, 2005).A large number of genomes with variations affecting the CDC N3 assay were also found (546 variations, 1.61%). Although they cannot be classified as critical based on the parameters defined in the present study, this data supports why the initial N3 CDC assay was removed from the official panel due to inconclusive results (Centers of Disease Control and Prevention, 2020a, 2020b).This same method of evaluation was carried out with the QIAstat-Dx SARS-CoV-2 Panel oligonucleotide sequences. The SARS-CoV-2 assay was originally developed as a real-time RT-PCR duplex assay covering two highly conserved target genes (RdRp and E) reported with the same fluorophore and showing a verified combined limit of detection (LoD) of 500 copies/mL in clinical samples (QIAstat-Dx Respiratory SARS-CoV-2 Panel, 2020). A total of 33,518 (99.11 %) of 33,819 matched with a 100% coverage all oligonucleotides included in the SARS-CoV-2 assays of the QIAstat-Dx Respiratory SARS-CoV-2 Panel. In contrast, 301 (0.89%) genomes showed a single variation affecting annealing for any oligonucleotide, and 35 (0.10%) of those 301 genomes contained a variation in any critical position of any primer or probe end. Among these latter ones, the most frequent variation consisted of a mismatch in the last position of the 3’-end of one of the primers (7 genomes, 0.02%). Because a mismatch in this position might impair the elongation PCR step (Stadhouders et al., 2010; Whiley and Sloots, 2005), this genomic mutation was further tested in vitro re-evaluating the LoD. A total of twenty replicates of quantified synthetic dsDNA reproducing the sequence containing this mutation were run at the LoD concentration (500 copies/mL) described in the publicly available QIAstat-Dx Respiratory SARS-CoV-2 Panel instructions for use (QIAstat-Dx Respiratory SARS-CoV-2 Panel, 2020), and 19 out of the 20 (95%) replicates were positive (Table S3) confirming the defined LoD. Therefore, the QIAstat-Dx SARS-CoV-2 assay remains highly specific and sensitive against SARS-CoV-2 even in light of genomic variations from the first three months of the COVID-19 outbreak (Visseaux et al., 2020).DISCUSSIONGenetic variability observed among SARS-CoV-2 genomes available until week 15, 2020 after the onset of the outbreak showed single nucleotide mutations affecting the annealing of all SARS-CoV-2 RT-PCR panels evaluated in this study. The majority of the annotated single nucleotide variations are predicted to have no effect on sensitivity at panel level, including those placed in critical positions. This was confirmed for the QIAstat-Dx SARS-CoV-2 Panel to show no effect on the LoD of the panel.Given that genetic variability in the SARS-CoV-2 genome is expected to increase based on the natural viral mutation and recombination rates, our results show that combination of more than one assay target in real-time RT-PCR SARS-CoV-2 panels can mitigate the risk of loss of sensitivity or specificity. In this regards, continuous monitoring of genomic variations is essential to provide a rapid response in case assay re-design is needed.AcknowledgementsWe thank all those who have contributed sequences to the GISAID database (https://www.gisaid.org/) and to NCBI database (http://www.ncbi.nlm.nih.gov/genbank/). We also thank the QIAstat-Dx Barcelona team for their support in their corresponding roles.Conflict of interests: LP, RP, MR, SNR, MJF,DM,MLF and JP are QIAGEN employees.No ethical approval was required to conduct this work. The work described in this paper was funded by the employer of the authors (QIAGEN).ReferencesAndersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med 2020. https://doi.org/10.1038/s41591-020-0820-9.Centers for Disease Control and Prevention (CDC). 2019-novel coronavirus (2019-nCoV) real-time rRT-PCR panel primers and probes. 2020a; Accessed: 09 Apr 2020. Available from: https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf.Centers for Disease Control and Prevention (CDC). CDC 2019-novel coronavirus (2019-nCoV) real-time RT-PCR diagnostic panel. 2020b; Accessed: 09 Apr 2020. Available from: https://www.fda.gov/media/134922/download.Chan JFW, Kok KH, Zhu Z, Chu H, To KKW, Yuan S, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect 2020; 9: 221-36. https://doi.org/10.1080/22221751.2020.1719902.Chu DKV, Pan Y, Cheng SMS, Hui KPY, Krishnan P, Liu Y, et al. Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia. Clin Chem 2020; 0(0):1-7. https://doi.org/10.1093/clinchem/hvaa029.Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, et al. Detection of 2019 novel coronavirus (2019-nCoV) by realtimeRT-PCR. Euro Surveill 2020; 25(3): pii=2000045. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045.Corman VM, Muth D, Niemeyer D, Drosten C. Hosts and sources of endemic human coronaviruses. Adv Virus Res 2018; 100:163-188. ISSN 0065-3527. https://doi.org/10.1016/bs.aivir.2018.01.001.Gorbalenya AE, Baker SC, Baric RS, de Groot RJ, Drosten C, Gulyaeva AA, et al. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020; 5: 536-44. https://doi.org/10.1038/s41564-020-0695-z.Lauring AS, Andino R. Quasispecies Theory and the Behavior of RNA Viruses. PLoS Pathog 2010; 6(7): e1001005. https://doi:10.1371/journal.ppat.1001005.Lippi G, Simundic AM, Plebani M. Potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease 2019 (COVID-19). Clin Chem Lab Med 2020; 20200285, eISSN 1437-4331, ISSN 1434-6621. https://doi.org/10.1515/cclm-2020-0285.National Microbiology Data Center (NMDC). Novel coronavirus national science and technology resource service system. 2020; Accessed: 09 Apr 2020.. Available from: http://nmdc.cn/nCov/en.QIAstat-Dx Respiratory SARS-CoV-2 Panel. QIAstat-Dx Respiratory SARS-CoV-2 Panel instructions for use (Handbook). 2020; Accessed: 09 Apr 2020. Available from: https://qiastat-dx.com/row/qiastat-dx-sars-cov-2/.Smith S, Vigilant L, Morin PA. The effects of sequence length and oligonucleotide mismatches on 5’ exonuclease assay efficiency. Nucleic Acids Res. 2002; 30(20): e111. https://doi.org/10.1093/nar/gnf110.Stadhouders R, Pas SD, Anber J, Voermans J, Mes THM, Schutten M. The effect of primer-template mismatches on the detection and quantification of nucleic acids using the 5’ nuclease assay. J Mol Diagn 2010; 12(1): 109-117. https://doi.org/10.2353/jmoldx.2010.090035.Sun J, He WT, Wang L, Lai A, Ji X, Zhai X et al. COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives. Trends Mol. Med0 2020; 1550. https://doi.org/10.1016/j.molmed.2020.02.008.The Open Science Prize. Nextstrain: Real-time tracking of pathogen evolution. Genomic epidemiology of novel coronavirus. 2020; Accessed: 09 Apr 2020. Available from: https://nextstrain.org/ncov.The University of Hong Kong (HKU), School of Public Health. Detection of 2019 novel coronavirus (2019-nCoV) in suspected human cases by RT-PCR. 2020; Accessed: 09 Apr 2020. Available from: https://www.who.int/docs/default-source/coronaviruse/peiris-protocol-16-1-20.pdf?sfvrsn=af1aac73_4.Visseaux B, Le Hingrat Q, Collin G, Bouzid D, Lebourgeois S, Le Pluart D et al. Evaluation of the QIAstat-Dx Respiratory SARS-CoV-2 Panel, the first rapid multiplex PCR commercial assay for SARS-CoV-2 detection. J Clin Microbiol 2020;JCM.00630-20. https//doi.org/10.1128/JCM.00630-20.Whiley DM and Sloots TP. Sequence variation in primer targets affects the accuracy of viral quantitative PCR. J Clin Virol 2005; 34: 104–107. https://doi.org/10.1016/j.jcv.2005.02.010.World Health Organization (WHO). Coronavirus disease 2019 (COVID-19) situation report -79. 2020a; Accessed: 09 Apr 2020. Available from: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/.World Health Organization (WHO). Laboratory testing for coronavirus disease 2019 (COVID-19) in suspected human cases. 2020b; Accessed: 09 Apr 2020. Available from: https://apps.who.int/iris/rest/bitstreams/1271387/retrieve.Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. A new coronavirus associated with human respiratory disease in China. Nature 2020; 579: 265–269. https://doi.org/10.1038/s41586-020-2008-3.Yi H. 2019 novel coronavirus is undergoing active recombination. Clin Infect Dis 2020; ciaa219. https://doi.org/10.1093/cid/ciaa219.Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 2020; 382(8): 727-33. https://doi.org/10.1056/NEJMoa2001017.Authors contributionsLP: Planned experiments, conceptualised the laboratory work, conceptualised the overall study, wrote the manuscript draft.MR: Planned and conducted experiments.RP: Planned and conducted experiments.SR: Contributed to overall study planning and review of the manuscript.MJ: Contributed to overall study planning and review of the manuscript.DM: Contributed to overall study conceptualization and review of the manuscript.MLF: Contributed to overall study planning and review of the manuscript.JP: Contributed to overall study conceptualization, co-wrote of the manuscript.Table 1. Description of earliest available SARS-CoV-2 RT-PCR assays RT-qPCR panel Assays included Target genes Description f References WHO panel a 3RdRp, E, Nthe E gene assay is used as the firstline screening tool, then followed by confirmatory testing with an RdRp gene assay. The N gene assay can eventually be analyzed as an additional confirmatory assay.Corman et al., 2020; World Health Organization, 2020bCDC (US) panel b 2NThis panel contains two monoplex assays (N1, N2) designed for specific detection of SARS-CoV-2. A specimen is considered positive for 2019-nCoV if both assays are positive, whereas if only one assay resulted positive the result is inconclusive and it should be retested.Centers of Disease Control and Prevention, 2020a, 2020bNMDC panel c 2RdRp, NThis panel contains two monoplex assays designed for specific detection of SARS-CoV-2. A specimen is considered positive for 2019-nCoV if both assays are positive.National Microbiology Data Center, 2020HKU panel d 2RdRp, NThe N gene RT-PCR is recommended as a screening assay and the Orf1b assay as a confirmatory one (the N gene assay is about 10 times more sensitive than the ORF-1b gene assay in detecting positive clinical specimens).Chu et al., 2020; The University of Hong Kong, 2020.QIAstat-Dx Panel e 2RdRp, EThis panel contains a Duplex assay in the same optical channel to report an additive performance (including CT and endpoint fluorescence values) of the two PCR assays and it discriminates SARS-CoV-2 detection from more than other 20 viruses and bacteria responsible for upper respiratory infections including other endemic coronavirusesQIAstat-Dx Respiratoyry SARS-CoV-2 Panel, 2020RdRp: RNA-dependent RNA polymerase gene (inside the Orf1ab polyprotein gene), E: envelop gene, N: Nucleocaspide gene.This panel was originally proposed by the Charité-Universitätsmedizin Berlin Institute of Virology (Corman et al., 2020), and then endorsed by the WHO (World Helath Organization, 2020b).Initial CDC panel contained one additional assay (N3) designed for universal detection of SARS-like coronaviruses (Centers of Disease Control and Prevention, 2020a) but has been removed due to inconclusive results based on low performance (Centers of Disease Control and Prevention, 2020b).National Microbiology Data Center (NMDC) works in collaboration with National Institute for Viral Disease Control and Prevention under Chinese Center for Disease Control and Prevention.The School of Public Health of the University of Hong Kong (HKU) developed the assay (Chu et al., 2020) and it was later established as official protocol under the WHO Network Laboratories (The University of Hong Kong, 2020).QIAstat-Dx Panel is a syndromic Point-of-Care system incorporating sample purification and real time RT-qPCR amplification for more than 20 viral and bacterial respiratory pathogens, including SARS-CoV-2.WHO and HKU assays are reactive with coronaviruses under the subgenus Sarbecovirus that includes 2019-nCoV, SARS-CoV and bat SARS-like coronaviruses. Since SARS was eliminated in humans since 2004, individuals with samples that are positive in these RT-PCR assays should be infected by the 2019-nCoV or its related animal coronaviruses.Table 2. Summary of genomic variants detected in complementary binding regions of earliest available SARS-CoV-2 RT-PCR assays. RT-qPCR panel assay Type Oligonucleotide name Number of genomes (%) with non-critical single variations Number of genomes (%) with high risk single variations WHO panelEFwE_Sarbeco_F10 (0.030%)2 (0.006%)aPE_Sarbeco_P134 (0.101%)9 (0.027%)bRevE_Sarbeco_R14 (0.4041%)-RdRpFwRdRp_SARSr-F95 (0.281%)5 (0.015%)cPRdRp_SARSr-P1126 (0.373%)2 (0.006%)dPRdRp_SARSr-P215 (0.044%)-RevRdRp_SARSr-R128 (0.378%)-NFwN_Sarbeco_F70 (0.207%)4 (0.012%)ePN_Sarbeco_P169 (0.204%)11 (0.033%)fRevN_Sarbeco_R119 (0.352%)1 (0.003%)g CDC (US) panelN1Fw2019-nCoV_N1-F40 (0.118%)3 (0.009%)hP2019-nCoV_N1-P53 (0.157%)353 (1.044%)iRev2019-nCoV_N1-R168 (0.497%)4 (0.012%)jN2Fw2019-nCoV_N2-F58 (0.172%)-P2019-nCoV_N2-P102 (0.302%)41 (0.121%)kRev2019-nCoV_N2-R41 (0.121%)-N3Fw2019-nCoV_N3-F344 (1.017%)l-P2019-nCoV_N3-P107 (0.316%)6 (0.018%)mRev2019-nCoV_N3-R86 (0.254%)3 (0.009%)n NMDC panelRdRpFwForward primer23 (0.068%)-PFluorescent probe48 (0.142%)10 (0.030%)oRevReverse primer30 (0.089%)1 (0.003%)pNFwForward primer337 (0.996%)8257 (24.415%)qPFluorescent probe15 (0.044%)3 (0.009%)rRevReverse primer56 (0.166%)5 (0.015%)s HKU panelRdRpFwHKU-ORF1b-nsp14F84 (0.248%)5 (0.015%)PHKU-ORF1b-nsp14P45 (0.133%)-RevHKU-ORF1b-nsp14R62 (0.183%)2 (0.006%)uNFwHKU-NF73 (0.216%)3 (0.009%)vPHKU-NP53 (0.157%)6 (0.018%)wRevHKU-NR83 (0.245%)2 (0.006%)x QIAstat-Dx PanelRdRpFwForward primer15 (0.044%)1 (0.003%)yPFluorescent probe133 (0.393%)12 (0.035%)zRevReverse primer27 (0.080%)3 (0.009%)aaEFwForward primer57 (0.169%)11 (0.032%)bbPFluorescent probe10 (0.030%)1 (0.003%)ccRevReverse primer24 (0.071%)7 (0.021%)dd TOTALS2,854 (8.434%)8,773 (25,941%)ACUMMULATED TOTAL11,627 (34.380%)Fw: Forward primer, P: Probe, Rev: Reverse primerTwo genome sequences with a mismatch in in the three last positions of the 3’-end (U to C and G to respectively).Nine genomes with a mismatch in the last three positions of the 5’-end (five A to G, and four C to U).Five genomes with a mismatch in the last three positions of the 3’-end (G to A, C to U, or G to U).Two genomes with multiple mismatches in the binding position of this probe (positions 1 (C to U), 7 (G to A), 10 (A to G), 12 (R to C), 21 (U to A) of the 5’-end)).Four genomes with a mismatch in any of the three last positions at the 3’-end (C to U, or U to C).Eleven genomes with a mismatch in position 2 of the 5’-end (C to U).One genome with a mismatch in the first position of the 3’-end (G to C).Three genomes with a mismatch in the second position of the 3’-end (A to C/G).A total of 353 genomes containing a mismatch in any of the last three positions of the 5’-end (C to A/U, C to U/G).Four genomes with a mismatch in the third position of the 3’-end (C to A).A total of 41 genomes with a mismatch in the first position of the 5’-end (A to U).A total of 292 genomes present the same mismatch in position 15 of the 3’-end (U to C).Six genomes with a mismatch in second (Y to G) or third (C to U) positions of the 5’-end.Three genomes with a mismatch in first (G to A) or second (U to A) positions of the 3’-end.Ten genomes with any mismatch in the last three positions of the 5’-end (C to A, C to U, G to A).A single genome with a mismatch in the second position of the 3’-end (G to A).A total of 8251 genomes with multiple three consecutive mismatches in positions 20,21,22 of the 3’-end, corresponding to positions 1, 2, 3 of the 5’-end (GGG to AAC). Six additional genomes with mismatches in any of the three last positions of the 3’-end.Three genomes with a mismatch in the second (U to C) or third (G to U) positions of the 5’-end.Five genomes with a mismatch in the first (G to A) or third (C to A/U) positions of the 3’-end.Five genomes with a mismatch in the second (C to U) or third (C to U) positions of the 3’-end.Two genomes with a mismatch in the second (U to C) or third (C to U) positions of the 3’-end.Three genomes with a mismatch in the third (U to C) position of the 3’-end.Six genomes with a mismatch in the second (C to A) or third (A to G) positions of the 5’-end.Two genomes with a mismatch in the second (U to C) or third (A to G) positions of the 3’-end.One mismatch in the third position of the 3’-end.Twelve genomes with a single mismatch in any of the three last positions of the 5’-end.Three genomes with a mismatch in the second position of the 3’-end.Seven genomes with a mismatch in the last position of the 3’-end, together with four additional genomes with a mismatch in the second or third positions.A single genome with a mismatch in the second position of the 5’-end.Six genomes with a mismatch in third position of the 3’-end, and one additional genome with a double mismatch in position 1


title: COVID-19: organoids go viral

text: The coronavirus disease-19 (COVID-19) pandemic underscores the threat posed by newly emerging viruses. Understanding the biology of novel viruses rests in large part on in vitro models that allow viral replication. Human and animal organoids are now proving their value as an experimental virology platform.


title: Air quality during the COVID-19: PM(2.5) analysis in the 50 most polluted capital cities in the world()

text: On December 31, 2019, the Chinese authorities reported to the World Health Organization (WHO) the outbreak of a new strain of coronavirus that causes a serious disease in the city of Wuhan, China. This outbreak was classified as SARS-CoV2 and is the cause of the COVID-19 disease. On March 11, 2020, the WHO declares it a Pandemic and today it is considered the greatest challenge in global health that humanity has faced since World War II and it is estimated that between 40 and 60% of the population worldwide will catch the virus. This has caused enormous challenges in countries around the world in social, economic, environmental and obviously health issues. These challenges are mainly due to the effects of the established quarantines in almost all capitals and major cities around the world, from Asia, Europe to America. However, these lockdown which began worldwide from January 23, have had a significant impact on the environment and on the air quality of cities as recently reported by NASA (National Aeronautics and Space Administration) and ESA (European Space Agency), with reductions according to them of up to 30% in some of the epicenters such as the case of Wuhan. Knowing that air pollution causes approximately 29% of lung cancer deaths, 43% of COPD deaths, and 25% of ischemic heart disease deaths, it is important to know the effects of quarantines in cities regarding air quality to take measures that favor populations and urban ecosystems when the emergency ends. Therefore, this paper describes the behavior of PM(2.5) emissions particulate matter from the 50 most polluted capital cities in the world according to the WHO, measured before-after the start of the quarantine. Likewise, the impact at the local and global level of this emissions behavior, which averaged 12% of PM(2.5) decrease in these cities.


title: Obesity and mortality of COVID-19. Meta-analysis

text: BACKGROUND: Obesity is a global disease with at least 2.8 million people dying each year as a result of being overweight or obese according to the world health organization figures. This paper aims to explore the links between obesity and mortality in COVID-19. METHODS: Electronic search was made for the papers studying obesity as a risk factor for mortality following COVID-19 infection. Three authors independently selected the papers and agreed for final inclusion. The outcomes were the age, gender, body mass index, severe comorbidities, respiratory support and the critical illness related mortality in COVID-19. 572 publications were identified and 42 studies were selected including one unpublished study data. Only 14 studies were selected for quantitative analysis. RESULTS: All the primary points but the gender are significantly associated with COVID-19 mortality. The age >70, [odd ratio (OR): 0.17, CI; 95%, P-value: <0.00001], gender [OR: 0.89; CI: 95%, P-value: 0.32], BMI > 25 kg/m(2) [OR: 3.68, CI: 95%, P-value: <0.003], severe comorbidities [OR: 1.84, CI:95%, P-value: <0.00001], advanced respiratory support [OR: 6.98, CI: 95%, P-value: <0.00001], and critical illness [OR: 2.03, CI: 95%, P-value: <0.00001]. CONCLUSIONS: Patients with obesity are at high risk of mortality from COVID-19 infection.


title: A Presentation of E-Cigarette Vaping Associated Lung Injury (EVALI) Caused by THC-Containing Electronic Smoking Device

text: Several cases have recently been reported concerning the development of a syndrome of acute lung injury associated with the use of electronic cigarettes, leading to respiratory failure and several deaths. We present a case of a young veteran who presented with e-cigarette vaping associated lung injury (EVALI) to a primary care clinic and who required subsequent inpatient admission and home oxygen therapy after discharge. The patient afterwards improved after a three-month course of steroids and cessation of THC-containing electronic cigarettes, consistent with previously reported cases. Furthermore, evidence on bronchoscopy and biopsy demonstrated intracellular lipid droplets in the patient’s macrophages. This outpatient case of EVALI prompts primary care providers to raise suspicion of this condition, and enquire about the use of e-cigarettes, particularly THC-containing vaping products. Furthermore, in the setting of the COVID-19 pandemic, similar clinical and radiographic presentations between COVID-19 and EVALI can be seen.


title: Detection of dicistroviruses RNA in blood of febrile Tanzanian children

text: Fever is the leading cause of paediatric outpatient consultations in Sub-Saharan Africa. Although most are suspected to be of viral origin, a putative causative pathogen is not identified in over a quarter of these febrile episodes. Using a de novo assembly sequencing approach, we report the detection (15.4%) of dicistroviruses (DicV) RNA in sera collected from 692 febrile Tanzanian children. In contrast, DicV RNA was only detected in 1/77 (1.3%) plasma samples from febrile Tanzanian adults, suggesting that children could represent the primary susceptible population. Estimated viral load by specific quantitative real-time RT–PCR assay ranged from < 1.32E3 to 1.44E7 viral RNA copies/mL serum. Three DicV full-length genomes were obtained, and a phylogenetic analyse on the capsid region showed the presence of two clusters representing tentative novel genus. Although DicV-positive cases were detected throughout the year, a significantly higher positivity rate was observed during the rainy season. This study reveals that novel DicV RNA is frequently detected in the blood of Tanzanian children, paving the way for further investigations to determine if DicV possibly represent a new agent in humans.


title: Role of angiotensin-converting enzyme (ACE) and ACE2 in a rat model of smoke inhalation induced acute respiratory distress syndrome

text: Abstract Smoke inhalation induced acute respiratory distress syndrome (ARDS) has become more and more common throughout the world and it is hard to improve the outcome. The present research was to investigate possible roles of angiotensin-converting enzyme (ACE) and ACE2 in lung injury resulted from smoke exposure. Rats were exposed to dense smoke to induce ARDS. Histological changes, blood gases, bronchoalveolar lavage fluids (BALF) and wet-to-dry weight were analyzed to evaluate lung injury after smoke inhalation; beside, we also measured the expression of ACE and ACE2 at different time points to explore the possible mechanism of those changes. The results showed that pH of arterial blood, partial blood oxygen (PaO2) and blood oxygen saturation (SO2) decreased after smoke inhalation at different time points (P <0.01); while, partial blood carbon dioxide (PaCO2), wet-to-dry weight ratio, leukocytes count, protein concentration and inflammatory cytokines in BALF increased after smoke exposure (P <0.01). More importantly, both immunohistochemical staining and Western blot results showed that ACE and ACE2 expression in lungs from the experimental groups significantly increased compared with that of the control group (P <0.05). This study indicated that inflammation pulmonary edema and histological changes resulted from smoke inhalation induced lung injury were possibly attributed to abnormal expression of ACE and ACE2 related pathway.


title: Equine arteritis virus

text: Abstract Equine arteritis virus (EAV) is a small, enveloped, positive-stranded RNA virus, in the family Arteriviridae , W.H.ich can infect both horses and donkeys. While the majority of EAV infections are asymptomatic, acutely infected animals may develop a wide range of clinical signs, including pyrexia, limb and ventral edema, depression, rhinitis, and conjunctivitis. The virus may cause abortion and has caused mortality in neonates. After natural EAV infection, most horses develop a solid, long-term immunity to the disease. Marzz and geldings eliminate the virus within 60 days, but 30 to 60% of acutely infected stallions will become persistently infected. These persistently infected animals maintain EAV within the reproductive tract, shed virus continuously in the semen, and can transmit the virus venereally. Mares infected venereally may not have clinical signs, but they shed large amounts of virus in nasopharyngeal secretions and in urine, which may result in lateral spread of the infection by an aerosol route. The consequences of venereally acquired infection are minimal, with no known effects on conception rate, but mares infected at a late stages of gestation may abort. Identification of carrier stallions is crucial to control the dissemination of EAV. The stallions can be identified by serological screening using a virus neutralization (VN) test. If positive at a titer of ≥ 1:4, the stallion should be tested for persistent infection by virus isolation from the sperm-rich fraction of the ejaculate, or by test mating Shedding stallions should not be used for breeding, or should be bred only to mares seropositive from a natural infection or from vaccination, the mares should be subsequently isolated from seronegative horses for three weeks after natural or artificial insemination. A live attenuated (ARVAC) and a formalin-inactivated (ARTERVAC) vaccine are available. Both vaccines induce virus-neutralizing antibodies, the presence of which correlates with protection from disease, abortion, and the development of a persistent infection. Serological investigations indicate that EAV has a worldwide distribution and that its prevalence is increasing. As a consequence, an increasing number of equine viral arteritis (EVA) outbreaks is being reported. This trend is likely to continue unless action is taken to slow or halt the transmission of this agent through semen.


COVID-19: The European institute of oncology as a “hub” centre for breast cancer surgery during the pandemic in Milan (Lombardy region, northern Italy) - A screenshot of the first month


title: Spillover of Swine Coronaviruses, United States

text: Porcine epidemic diarrhea virus, a pathogen first detected in US domestic swine in 2013, has rapidly spilled over into feral swine populations. A better understanding of the factors associated with pathogen emergence is needed to better manage, and ultimately prevent, future spillover events from domestic to nondomestic animals.


title: Prediction of novel mouse TLR9 agonists using a random forest approach

text: BACKGROUND: Toll-like receptor 9 is a key innate immune receptor involved in detecting infectious diseases and cancer. TLR9 activates the innate immune system following the recognition of single-stranded DNA oligonucleotides (ODN) containing unmethylated cytosine-guanine (CpG) motifs. Due to the considerable number of rotatable bonds in ODNs, high-throughput in silico screening for potential TLR9 activity via traditional structure-based virtual screening approaches of CpG ODNs is challenging. In the current study, we present a machine learning based method for predicting novel mouse TLR9 (mTLR9) agonists based on features including count and position of motifs, the distance between the motifs and graphically derived features such as the radius of gyration and moment of Inertia. We employed an in-house experimentally validated dataset of 396 single-stranded synthetic ODNs, to compare the results of five machine learning algorithms. Since the dataset was highly imbalanced, we used an ensemble learning approach based on repeated random down-sampling. RESULTS: Using in-house experimental TLR9 activity data we found that random forest algorithm outperformed other algorithms for our dataset for TLR9 activity prediction. Therefore, we developed a cross-validated ensemble classifier of 20 random forest models. The average Matthews correlation coefficient and balanced accuracy of our ensemble classifier in test samples was 0.61 and 80.0%, respectively, with the maximum balanced accuracy and Matthews correlation coefficient of 87.0% and 0.75, respectively. We confirmed common sequence motifs including ‘CC’, ‘GG’,‘AG’, ‘CCCG’ and ‘CGGC’ were overrepresented in mTLR9 agonists. Predictions on 6000 randomly generated ODNs were ranked and the top 100 ODNs were synthesized and experimentally tested for activity in a mTLR9 reporter cell assay, with 91 of the 100 selected ODNs showing high activity, confirming the accuracy of the model in predicting mTLR9 activity. CONCLUSION: We combined repeated random down-sampling with random forest to overcome the class imbalance problem and achieved promising results. Overall, we showed that the random forest algorithm outperformed other machine learning algorithms including support vector machines, shrinkage discriminant analysis, gradient boosting machine and neural networks. Due to its predictive performance and simplicity, the random forest technique is a useful method for prediction of mTLR9 ODN agonists.


title: Coronavirus Disease 2019 (COVID-19): A Perspective from China

text: In December 2019, an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection occurred in Wuhan, Hubei Province, China and spread across China and beyond. On February 12, 2020, WHO officially named the disease caused by the novel coronavirus as Coronavirus Disease 2019 (COVID-19). Since most COVID-19 infected patients were diagnosed with pneumonia and characteristic CT imaging patterns, radiological examinations have become vital in early diagnosis and assessment of disease course. To date, CT findings have been recommended as major evidence for clinical diagnosis of COVID-19 in Hubei, China. This review focuses on the etiology, epidemiology, and clinical symptoms of COVID-19, while highlighting the role of chest CT in prevention and disease control. A full translation of this article in Chinese is available in the supplement. - 请见䃼充资料阅读文章中文版∘


title: An epidemic CC1-MRSA-IV clone yields false-negative test results in molecular MRSA identification assays: a note of caution, Austria, Germany, Ireland, 2020

text: We investigated why a clinical meticillin-resistant Staphylococcus aureus (MRSA) isolate yielded false-negative results with some commercial PCR tests for MRSA detection. We found that an epidemic European CC1-MRSA-IV clone generally exhibits this behaviour. The failure of the assays was attributable to a large insertion in the orfX/SCCmec integration site. To ensure the reliability of molecular MRSA tests, it is vital to monitor emergence of new SCCmec types and junction sites.


title: Tuberculose em profissionais de saúde de um serviço hospitalar

text: Abstract Introduction: Tuberculosis (TB) is considered an occupational disease in health care workers (HCW) and its transmission in health care facilities is an important concern. Some hospital departments are at higher risk of infection. Objective: To describe TB cases detected after TB screening in HCW from a hospital department (Ear, Nose and Throat – ENT) who had had contact with active TB cases. Material and methods: All HCW (73) from Hospital São João’s ENT Unit who had been in contact with two in-patients with active TB underwent TB screening. Those who had symptoms underwent chest X-ray and mycobacteriological sputum exam. Results: Of 73 HCW who underwent TB screening, TB diagnosis was established in 9 (8 female; median age: 30 years; 1 doctor, 6 nurses, 2 nursing auxiliaries). Pulmonary TB was found in 8 and extra-pulmonary TB in 1. Microbiology diagnosis was obtained in 7 cases by sputum smear, n=2; culture exam in bronchial lavage, n=4 and histological exam of pleural tissue, n=1. In 4 cases, Mycobacterium tuberculosis genomic DNA was extracted from cultures and molecular typing was done. All cases had identical MIRU types, which allowed identification of the epidemiological link. Conclusion: Nosocomial TB is prominent and efforts should be made to implement successful infection control measures in health care facilities and an effective TB screening program in HCW. Molecular typing of Mycobacterium tuberculosis facilitates cluster identification. Rev Port Pneumol 2007; XIII (6): 789-799


title: RNA structure analysis of alphacoronavirus terminal genome regions

text: Abstract Coronavirus genome replication is mediated by a multi-subunit protein complex that is comprised of more than a dozen virally encoded and several cellular proteins. Interactions of the viral replicase complex with cis-acting RNA elements located in the 5′ and 3′-terminal genome regions ensure the specific replication of viral RNA. Over the past years, boundaries and structures of cis-acting RNA elements required for coronavirus genome replication have been extensively characterized in betacoronaviruses and, to a lesser extent, other coronavirus genera. Here, we review our current understanding of coronavirus cis-acting elements located in the terminal genome regions and use a combination of bioinformatic and RNA structure probing studies to identify and characterize putative cis-acting RNA elements in alphacoronaviruses. The study suggests significant RNA structure conservation among members of the genus Alphacoronavirus but also across genus boundaries. Overall, the conservation pattern identified for 5′ and 3′-terminal RNA structural elements in the genomes of alpha- and betacoronaviruses is in agreement with the widely used replicase polyprotein-based classification of the Coronavirinae, suggesting co-evolution of the coronavirus replication machinery with cognate cis-acting RNA elements.


title: Hypothesis: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers may increase the risk of severe COVID-19

text: Intravenous infusions of angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) in experimental animals increase the numbers of angiotensin-converting enzyme 2 (ACE2) receptors in the cardiopulmonary circulation. ACE2 receptors serve as binding sites for SARS-CoV-2 virions in the lungs. Patients who take ACEIs and ARBS may be at increased risk of severe disease outcomes due to SARS-CoV-2 infections.


Obesity and Stroke in the COVID19 era


title: The COVID-19 Virtual Idea Blitz: Marshaling social entrepreneurship to rapidly respond to urgent grand challenges

text: In response to societal grand challenges, professors have unique opportunities to effect change, repurposing their expertise to deploy relevant, timely, practical, and research-backed knowledge for the betterment of communities. Drawing on scholarship on postcrisis organizing, the entrepreneurial hustle, and social entrepreneurship, we provide a firsthand, real-time case description of a three-day “virtual idea blitz” organized in response to the COVID-19 crisis. The event was organized and executed in less than a week and ultimately involved 200 individuals, including entrepreneurs, coders, medical doctors, venture capitalists, industry professionals, students, and professors from around the world. By the end of the weekend, 21 ideas with corresponding pitches were developed in five thematic areas: health needs, education, small businesses, community, and purchasing. We describe how the community was rapidly rallied, and we discuss the key learning outcomes of this spontaneous entrepreneurial endeavor. We provide evidence from participants and mentors that showcases the value of the time-compressed virtual idea blitz in accelerating social entrepreneurial action. We offer practical guidance to academic, community, and professional institutions that would like to replicate or build upon our approach to stimulate the formation of community-based and coordinating efforts to thwart the ongoing threat of COVID-19, as well as other societal challenges that might emerge in the future.


title: Porcine deltacoronavirus induces apoptosis in swine testicular and LLC porcine kidney cell lines in vitro but not in infected intestinal enterocytes in vivo

text: Abstract We compared the mechanisms of porcine delatacoronavirus (PDCoV) induced death of infected enterocytes in vivo and infected LLC porcine kidney (LLC-PK) and swine testicular (ST) cells in vitro. We conducted histologic analysis and immunofluorescence (IF) staining for the detection of PDCoV antigens, and TUNEL assay in singly or serially cut tissue sections from the small and large intestines of four, 11- to 14-day-old gnotobiotic pigs, inoculated orally with 8.8–11.0log10 genomic equivalents (GE) of US PDCoV strains OH-FD22 or OH-FD100 (n =3), or mock (n =1). Similar comparative assays were done on LLC-PK and ST cells inoculated with the cell-adapted PDCoV strain OH-FD22-P44 (passage 44) in cell culture medium with 2.5–10μg/ml of trypsin and 1% pancreatin, respectively. At post-inoculation days 3–4, infected pigs showed severe watery diarrhea and/or vomiting and mainly, diffuse, severe atrophic enteritis, with mild to moderate cytoplasmic vacuolation of the enteroctyes lining the atrophied villous epithelium. By IF, PDCoV antigens were evident in villous or crypt epithelial cells. No PDCoV antigen-positive, small and large intestinal villous or crypt epithelial cells, of which cytoplasm was also either vacuolated or morphologically normal, showed positive TUNEL staining. In contrast, by double IF and TUNEL staining, most of the TUNEL-positive signals (apoptotic nuclear fragmentation) were found in PDCoV antigen-positive LLC-PK and ST cells that also showed cytopathic effects, such as cell rounding, detachment and clumping in clusters. Secondary annexin V/propidium iodide (PI) staining revealed increased numbers of annexin V- or PI-positive LLC-PK and ST cells at 21h after inoculation, compared to the negative controls. Thus, PDCoV does not induce apoptosis in the infected intestinal enterocytes in vivo, but in two infected cell lines of swine origin, LLC-PK and ST cells.


title: Conventional and nonconventional roles of the nucleolus

text: Abstract As the most prominent of subnuclear structures, the nucleolus has a well-established role in ribosomal subunit assembly. Additional nucleolar functions, not related to ribosome biogenesis, have been discovered within the last decade. Built around multiple copies of the genes for preribosomal RNA (rDNA), nucleolar structure is largely dependent on the process of ribosome assembly. The nucleolus is disassembled during mitosis at which time preribosomal RNA transcription and processing are suppressed; it is reassembled at the end of mitosis in part from components preserved from the previous cell cycle. Expression of preribosomal RNA (pre-rRNA) is regulated by the silencing of individual rDNA genes via alterations in chromatin structure or by controlling RNA polymerase I initiation complex formation. Preribosomal RNA processing and posttranscriptional modifications are guided by a multitude of small nucleolar RNAs. Nearly completed ribosomal subunits are exported to the cytoplasm by an established nuclear export system with the aid of specialized adapter molecules. Some preribosomal and nucleolar components are transiently localized in Cajal bodies, presumably for modification or assembly. The nonconventional functions of nucleolus include roles in viral infections, nuclear export, sequestration of regulatory molecules, modification of small RNAs, RNP assembly, and control of aging, although some of these functions are not well established. Additional progress in defining the mechanisms of each step in ribosome biogenesis as well as clarification of the precise role of the nucleolus in nonconventional activities is expected in the next decade.


title: Potential of Arbidol for Post-exposure Prophylaxis of COVID-19 Transmission—A Preliminary Report of a Retrospective Cohort Study

text: The efficient transmission of severe acute respiratory syndrome-2 coronavirus (SARS-CoV-2) from patients to health care workers or family members has been a worrisome and prominent feature of the ongoing outbreak. On the basis of clinical practice and in-vitro studies, we postulated that post-exposure prophylaxis (PEP) using Arbidol is associated with decreased infection among individuals exposed to confirmed cases of COVID-19 infection. We conducted a retrospective cohort study on family members and health care workers who were exposed to patients confirmed to have SARS-CoV-2 infection by real-time RT-PCR and chest computed tomography (CT) from January 1 to January 16, 2020. The last follow-up date was Feb. 26, 2020. The emergence of fever and/or respiratory symptoms after exposure to the primary case was collected. The correlations between post-exposure prophylaxis and infection in household contacts and health care workers were respectively analyzed. A total of 66 members in 27 families and 124 health care workers had evidence of close exposure to patients with confirmed COVID-19. The Cox regression based on the data of the family members and health care workers with Arbidol or not showed that Arbidol PEP was a protective factor against the development of COVID-19 (HR 0.025, 95% CI 0.003–0.209, P=0.0006 for family members and HR 0.056, 95% CI 0.005–0.662, P=0.0221 for health care workers). Our findings suggest Arbidol could reduce the infection risk of the novel coronavirus in hospital and family settings. This treatment should be promoted for PEP use and should be the subject of further investigation.


title: Early transmission dynamics of COVID-19 in a southern hemisphere setting: Lima-Peru: February 29th–March 30th, 2020.

text: The COVID-19 pandemic that emerged in Wuhan China has generated substantial morbidity and mortality impact around the world during the last four months. The daily trend in reported cases has been rapidly rising in Latin America since March 2020 with the great majority of the cases reported in Brazil followed by Peru as of April 15th, 2020. Although Peru implemented a range of social distancing measures soon after the confirmation of its first case on March 6th, 2020, the daily number of new COVID-19 cases continues to accumulate in this country. We assessed the early COVID-19 transmission dynamics and the effect of social distancing interventions in Lima, Peru. We estimated the reproduction number, R, during the early transmission phase in Lima from the daily series of imported and autochthonous cases by the date of symptoms onset as of March 30th, 2020. We also assessed the effect of social distancing interventions in Lima by generating short-term forecasts grounded on the early transmission dynamics before interventions were put in place. Prior to the implementation of the social distancing measures in Lima, the local incidence curve by the date of symptoms onset displays near exponential growth dynamics with the mean scaling of growth parameter, p, estimated at 0.9 (95%CI: 0.9,1.0) and the reproduction number at 2.3 (95% CI: 2.0, 2.5). Our analysis indicates that school closures and other social distancing interventions have helped slow down the spread of the novel coronavirus, with the nearly exponential growth trend shifting to an approximately linear growth trend soon after the broad scale social distancing interventions were put in place by the government. While the interventions appear to have slowed the transmission rate in Lima, the number of new COVID-19 cases continue to accumulate, highlighting the need to strengthen social distancing and active case finding efforts to mitigate disease transmission in the region.


Forgetting ‘routine’ DVT and stroke during COVID-19 is a parallel pandemic that will be costly if ignored


title: Is the Saudi public aware of Middle East respiratory syndrome?

text: Summary To limit the spread of Middle East respiratory syndrome coronavirus (MERS-CoV) in Saudi Arabia, the Ministry of Health tried to raise public awareness using different public campaigns. We aimed to measure public awareness of MERS in Saudi Arabia. A cross-sectional study was conducted between May and June 2014 using a newly designed Arabic questionnaire that was distributed and completed online. We analyzed the response of 1149 respondents across Saudi Arabia. We found that 97% of the participants were aware of MERS. In addition, 72% realized that coughing and sneezing could spread the infection. Furthermore, 83% thought that some patients with MERS could be cured. Moreover, 62% knew that no vaccine can prevent the disease. However, only 36% realized that taking antibiotics will not stop the infection, and only 41% recognized that no medication has yet been manufactured to treat it. Regarding protection measures, 74% used hand sanitizers, 43% avoided crowded places, and 11% wore masks in public places. Moreover, only 47% knew that bats and camels are the primary source of the virus. As anticipated, this level of awareness varied between the different categories of the studied population. Female, married, older, and more educated participants were significantly more knowledgeable about the disease. Public awareness of MERS is generally sufficient. However, some false beliefs about treatment were fairly common. In addition, almost half of the population remains unaware that bats and camels are the most likely sources of the virus.


title: Healthcare Digitalization and Pay-For-Performance Incentives in Smart Hospital Project Financing

text: This study aims to explore the impact of healthcare digitalization on smart hospital project financing (PF) fostered by pay-for-performance (P4P) incentives. Digital platforms are a technology-enabled business model that facilitates exchanges between interacting agents. They represent a bridging link among disconnected nodes, improving the scalable value of networks. Application to healthcare public–private partnerships (PPPs) is significant due to the consistency of digital platforms with health issues and the complexity of the stakeholder’s interaction. In infrastructural PPPs, public and private players cooperate, usually following PF patterns. This relationship is complemented by digitized supply chains and is increasingly patient-centric. This paper reviews the literature, analyzes some supply chain bottlenecks, addresses solutions concerning the networking effects of platforms to improve PPP interactions, and investigates the cost–benefit analysis of digital health with an empirical case. Whereas diagnostic or infrastructural technology is an expensive investment with long-term payback, leapfrogging digital applications reduce contingent costs. “Digital” savings can be shared by key stakeholders with P4P schemes, incentivizing value co-creation patterns. Efficient sharing may apply network theory to a comprehensive PPP ecosystem where stakeholding nodes are digitally connected. This innovative approach improves stakeholder relationships, which are re-engineered around digital platforms that enhance patient-centered satisfaction and sustainability. Digital technologies are useful even for infectious disease surveillance, like that of the coronavirus pandemic, for supporting massive healthcare intervention, decongesting hospitals, and providing timely big data.


title: Generation and characterization of anti-α-enolase single-chain antibodies in chicken

text: Abstract It was previously reported that up-regulation of α-enolase protein was detected in 65% of patients with non-small cell lung cancers (NSCLC). Moreover, a high titer of anti-α-enolase antibodies was developed in a smaller proportion (7.4%) of these patients than in non-tumor-associated patients and healthy subjects. In the present study, we characterized polyclonal and single-chain variable fragment (scFv) anti-α-enolase antibodies from immunized chickens. The E. coli-derived recombinant α-enolase protein was purified to its high homogenicity as verified by SDS-PAGE. After the 4th immunization, a high titer of specific polyclonal anti-α-enolase antibodies was elicited in immunized chickens and specifically recognized the purified human α-enolase antigen as determined by Western blot and ELISA. The expressed heavy and light chain variable genes (VH and VL) were isolated from spleen B cells and amplified to construct phage antibody libraries containing scFv molecules. After four rounds of panning selection, the scFv antibodies of randomly chosen clones were expressed and their binding specificity to α-enolase protein was verified using competitive ELISA, flow cytometry and immunofluorescence staining. Nucleotide sequence analysis from 10 α-enolase binding clones showed that 3 (30%) clones used identical heavy and light genes for scFv antibody expression, as represented by EnL5. Notably, amino acid changes in complementarity-determining regions (CDRs) were more frequently observed than those in framework regions (FRs) in all clones, indicating a strong affinity selection through mutations. All together, it is believed that these polyclonal and scFv IgY antibodies may be helpful in the development of molecular diagnostic and therapeutic agents for lung cancers in the future.


Student’s Perception of Online Learning during COVID Pandemic


title: Validation of Assays to Monitor Immune Responses in the Syrian Golden Hamster (Mesocricetus auratus)

text: The Syrian Golden hamster (Mesocricetus auratus) is a valuable but under-utilized animal model for studies of human viral pathogens such as bunyaviruses, arenaviruses, flaviviruses, henipaviruses, and SARS-coronavirus. A lack of suitable reagents and specific assays for monitoring host responses has limited the use of this animal model to clinical observations, pathology and humoral immune responses. The objective of this study was to establish and validate assays to monitor host immune responses in the hamster including important pro-inflammatory, anti-inflammatory and innate immune responses, as well as markers of apoptosis, cell proliferation, cell junction integrity and coagulation. Commercially available mouse and rat ELISA and luminex panels were screened for potential cross-reactivity, but were found to be of limited value for studying host responses in hamsters. Subsequently, quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assays for the detection of 51 immune-related and four internal reference genes were developed. To validate the immune-related assays, hamsters were infected with vesicular stomatitis virus (VSV), Indiana species, or treated with lipopolysaccharide (LPS) and host immune responses were monitored in selected organs. Ribosomal protein L18 was identified as the most stable internal reference gene. In conclusion, these new assays will greatly improve the use of the hamster as an important small animal model in infectious disease research.


title: Allelic Variation in the Toll-Like Receptor Adaptor Protein Ticam2 Contributes to SARS-Coronavirus Pathogenesis in Mice

text: Host genetic variation is known to contribute to differential pathogenesis following infection. Mouse models allow direct assessment of host genetic factors responsible for susceptibility to Severe Acute Respiratory Syndrome coronavirus (SARS-CoV). Based on an assessment of early stage lines from the Collaborative Cross mouse multi-parent population, we identified two lines showing highly divergent susceptibilities to SARS-CoV: the resistant CC003/Unc and the susceptible CC053/Unc. We generated 264 F2 mice between these strains, and infected them with SARS-CoV. Weight loss, pulmonary hemorrhage, and viral load were all highly correlated disease phenotypes. We identified a quantitative trait locus of major effect on chromosome 18 (27.1–58.6 Mb) which affected weight loss, viral titer and hemorrhage. Additionally, each of these three phenotypes had distinct quantitative trait loci [Chr 9 (weight loss), Chrs 7 and 12 (virus titer), and Chr 15 (hemorrhage)]. We identified Ticam2, an adaptor protein in the TLR signaling pathways, as a candidate driving differential disease at the Chr 18 locus. Ticam2(−/−) mice were highly susceptible to SARS-CoV infection, exhibiting increased weight loss and more pulmonary hemorrhage than control mice. These results indicate a critical role for Ticam2 in SARS-CoV disease, and highlight the importance of host genetic variation in disease responses.


title: Expression of viral and myelin gene transcripts in a murine CNS demyelinating disease caused by a coronavirus

text: C57BI/6N mice develop a CNS demyelinating disease when inoculated intracranially at 4 weeks of age with the A59 strain of mouse hepatitis virus (MHV‐A59). In order to explore the virus‐host interactions, the histological features of the demyelinating disease were correlated with the spatial and temporal distribution of viral transcripts and the expression of oligodendrocyte‐specific genes (myelin basic protein, proteolipid protein, myelin‐associated glycoprotein, and 2′, 3′ cyclic nucleotide 3′‐phosphohydrolase) in the spinal cord of diseased mice. Three distinct phases in the disease were identified. In the first phase, 1 week postinfection (1 WPI), virus replication was widespread in both gray and white matter but was preferentially occurring in glial cells. In the ventral and dorsal root zones where viral transcripts were most abundant, all myelin gene transcripts were decreased before demyelination was seen. During the second phase of the disease (2–3 WPI), viral transcripts decreased in abundance and became restricted to the white matter. Numerous demyelinating lesions were observed and were characterized by inflammatory cells, paucity of oligodendrocytes, and a profound decrease of all myelin gene transcripts. In the third phase of the disease (4–6 WPI) no viral transcripts were detected, and remyelination began. In the lesions and the tissue surrounding them, transcripts of all myelin genes increased to levels above normal. The increased expression of myelin gene transcripts occurred in a synchronized manner and with a cellular distribution reminiscent of that seen in developmental myelination. These molecular events correlated with efficient remyelination and clinical recovery in this murine demyelinating disease.


title: Response of rat tracheal epithelium to ozone and oxygen exposure in vitro

text: Abstract Although ozone-induced epithelial injury in vivo has been morphologically characterized, effects of gaseous oxidants on respiratory epithelium in organ culture, where tissue organization is maintained but systemic influences are eliminated, have not been thoroughly investigated. In this study, we exposed tracheal organ cultures from rats to 95% oxygen and 1 ppm ozone, alone and in combination, to determine (1) whether epithelial responses to ozone similar to those observed in vivo occur in airways separated from systemic physiologic, secretory, and inflammatory reactions; (2) whether concentrations of oxygen sufficient to potentially cause oxidant injury result in morphologic epithelial alterations similar to those that occur in ozone toxicity; and (3) if the combined oxidant insult of oxygen and ozone results in more severe damage to the tracheal epithelium than occurs with ozone in air. Tracheal organ cultures were exposed to filtered air and 5% carbon dioxide; filtered air, 5% carbon dioxide, and 1 ppm ozone; 95% oxygen and 5% carbon dioxide; or 95% oxygen, 5% carbon dioxide, and 1 ppm ozone for 96 hr. Light- and quantitative electron-microscopic evaluation showed that epithelia to 1 ppm ozone in air exhibited loss of ciliated cells and ciliated cell damage. The epithelia exposed to 95% oxygen and 5% carbon dioxide were pseudostratified, columnar, ciliated, and hyperplastic. Epithelia exposed to 95% oxygen plus 1 ppm ozone were stratified and nonciliated or very sparsely ciliated. The predominant cell types in epithelia exposed to oxygen plus ozone were serous cells and metaplastic cells, and focal aggregates of adherent necrotic cells were present. We conclude that there was a synergism between oxygen and ozone exposure leading to enhanced epithelial injury and metaplasia.


title: β-Endorphin alters a viral induced central nervous system disease in normal mice but not in nude mice

text: Abstract A single intracerebroventricular injection of 100 ng of β-endorphin altered the course of the central nervous system (CNS) infection of a temperature-sensitive mutant of vesicular stomatitis virus (VSV), tsG31-KS5. When mice were administered β-endorphin and then 24 h later infected intracerebrally with tsG31-Ks5 VSV, 70% of the animals died within 8 days of infection. In comparison, less than 10% of the animals had died after 21 days when infected with tsG31-KS5 VSV alone. When mice were injected with β-endorphin and tsG31-KS5 VSV simultaneously, or with β-endorphin 21 days after infection, the more aggressive clinical disease was not observed. Superficially, the more lethal disease induced by β-endorphin appeared to be a result of a mild hypothermia caused by the neuropeptide. β-Endorphin, however, did not influence the disease in nude (nu/nu) mice even though their core temperatures were reduced to an extent similar to that of BALB/c (+/+) mice, implicating the involvement of T lymphocytes in the alteration of the course of infection in normal mice.


title: Infections in Chronic Lung Diseases

text: Chronic lung diseases are prevalent worldwide and cause significant mortality and suffering. This article discusses infections that occur in three chronic lung diseases: chronic obstructive pulmonary disease, bronchiectasis, and cystic fibrosis. Rather than discussing the role of infections as etiology of these diseases, this article focuses on infections that occur in the background of established chronic lung disease.


title: Antibody germline characterization of cross-neutralizing human IgGs against 4 serotypes of dengue virus

text: Abstract Dengue virus (DENV), a re-emerging virus, constitutes the largest vector-borne disease virus, with 50–100 million cases reported every year. Although DENV infection induces lifelong immunity against viruses of the same serotypes, the subsequent infection with the heterologous serotypes can cause more severe form of the disease, such as Dengue Haemorrhagic Fever (DHF) or Dengue Shock Syndrome (DSS). However, there is neither approved vaccine nor specific drugs available to treat this disease. In this study, previously developed 19 human monoclonal antibodies (HuMAbs) showing strong to moderate cross neutralizing activity were selected. Most of them (13/19) were targeted to domain II of envelop glycoprotein. To understand and clarify the recognition properties, the maturation mechanisms comprising Variable/Diversity/Joining (VDJ) recombination, Variable Heavy (VH)/Variable Light (VL) chain pairing, variability at junctional site, and somatic hypermutation (SHM) of those antibodies were studied and compared with their predecessor germline sequences. IMGT/V-QUEST database was applied to analyze the isolated VH and VL sequences. To confirm the correction of isolated VH/VL, 3 HuMAbs (1A10H7, 1B3B9, 1G7C2) was transiently expressed in HEK293T cell. All three clones of the expressed recombinant IgG (rIgG) showed the same binding and neutralizing activity as same as those from hybridomas. The data obtained in this study will elucidate the properties of those HuMAbs for further genetic modification, and its binding epitopes.


title: Further characterization of mouse hepatitis virus RNA-dependent RNA polymerases

text: Abstract Two temporally and enzymatically distinct RNA-dependent RNA polymerase activities associated with membranes of the mouse hepatitis virus (MHV)-infected cells have been identified previously [Brayton et al., J. Virol. 42, 847–853 (1982)]. In this paper, the subcellular distribution and functions of these two polymerases were examined. Fractionation of the postnuclear membranes by sucrose gradient sedimentation showed that the early polymerase activity (detected at 1 hr p.i.) was homogeneous, while the late polymeras e (6 hr p.i.) was associated with two distinct membrane fractions. The early polymerase synthesized a single RNA species of viral genomic size and negative sense. In contrast, the light peak of the late polymerase synthesized genomic-sized RNA of positive sense, while the heavy peak of the activity synthesized positive-sensed genomic and subgenomic mRNAs. These findings suggest that the light peak of the late polymerase represents a replication complex while the heavy peak represents a transcription complex. They also establish the essential features of the mode of replication of MHV.


title: Food is medicine: actions to integrate food and nutrition into healthcare

text: Sarah Downer and colleagues review new efforts to incorporate food and nutrition into prevention, management, and treatment of diet related disease in healthcare systems


title: An immunosuppressed Syrian golden hamster model for SARS-CoV infection

text: Several small animal models have been developed for the study of severe acute respiratory syndrome coronavirus (SARS-CoV) replication and pathogenesis. Syrian golden hamsters are among the best small animal models, though little clinical illness and no mortality are observed after virus infection. Cyclophosphamide was used to immunosuppress hamsters leading to a prolonged disease course and higher mortality after SARS-CoV infection. In addition, there was a significant weight loss, expanded tissue tropism, and increased viral pathology in the lung, heart, kidney, and nasal turbinate tissues. Infection with recombinant SARS-CoV viruses bearing disruptions in the gene 7 coding region showed no significant change in replication kinetics, tissue tropism, morbidity, or mortality suggesting that the ORF7a (7a) and ORF7b (7b) proteins are not required for virus replication in immunosuppressed hamsters. This modified hamster model may provide a useful tool for SARS-CoV pathogenesis studies, evaluation of antiviral therapy, and analysis of additional SARS-CoV mutants.


title: The Second Worldwide Wave of Interest in Coronavirus since the COVID-19 Outbreaks in South Korea, Italy and Iran: A Google Trends Study

text: The recent emergence of a new coronavirus, COVID-19, has gained extensive coverage in public media and global news. As of 24 March 2020, the virus has caused viral pneumonia in tens of thousands of people in Wuhan, China, and thousands of cases in 184 other countries and territories. This study explores the potential use of Google Trends (GT) to monitor worldwide interest in this COVID-19 epidemic. GT was chosen as a source of reverse engineering data, given the interest in the topic. Current data on COVID-19 is retrieved from (GT) using one main search topic: Coronavirus. Geographical settings for GT are worldwide, China, South Korea, Italy and Iran. The reported period is 15 January 2020 to 24 March 2020. The results show that the highest worldwide peak in the first wave of demand for information was on 31 January 2020. After the first peak, the number of new cases reported daily rose for 6 days. A second wave started on 21 February 2020 after the outbreaks were reported in Italy, with the highest peak on 16 March 2020. The second wave is six times as big as the first wave. The number of new cases reported daily is rising day by day. This short communication gives a brief introduction to how the demand for information on coronavirus epidemic is reported through GT.


title: Stochastic and spatio-temporal analysis of the Middle East Respiratory Syndrome outbreak in South Korea, 2015

text: South Korea was free of the Middle East Respiratory Syndrome (MERS) until 2015. The MERS outbreak in South Korea during 2015 was the largest outbreak of the Coronavirus outside the Middle East. The major characteristic of this outbreak is inter- or intra-hospital transmission. This recent MERS outbreak in South Korea is examined and assessed in this paper. The main objectives of the study is to characterize the pattern of the MERS outbreak in South Korea based on a basic reproductive ratio, the probability of ultimate extinction of the disease, and the spatio-temporal proximity of occurrence between patients. The survival function method and stochastic branching process model are adapted to calculate the basic reproductive ratio and the probability of ultimate extinction of the disease. We further investigate the occurrence pattern of the outbreak using a spatio-temporal autocorrelation function.


title: Development of a recombinant replication-deficient rabies virus-based bivalent-vaccine against MERS-CoV and rabies virus and its humoral immunogenicity in mice

text: Middle East respiratory syndrome-coronavirus (MERS-CoV) is an emerging virus that causes severe disease with fatal outcomes; however, there are currently no approved vaccines or specific treatments against MERS-CoV. Here, we developed a novel bivalent vaccine against MERS-CoV and rabies virus (RV) using the replication-incompetent P-gene-deficient RV (RVΔP), which has been previously established as a promising and safe viral vector. MERS-CoV spike glycoprotein comprises S1 and S2 subunits, with the S1 subunit being a primary target of neutralizing antibodies. Recombinant RVΔP, which expresses S1 fused with transmembrane and cytoplasmic domains together with 14 amino acids from the ectodomains of the RV-glycoprotein (RV-G), was developed using a reverse genetics method and named RVΔP-MERS/S1. Following generation of RVΔP-MERS/S1 and RVΔP, our analysis revealed that they shared similar growth properties, with the expression of S1 in RVΔP-MERS/S1-infected cells confirmed by immunofluorescence and western blot, and the immunogenicity and pathogenicity evaluated using mouse infection experiments. We observed no rabies-associated signs or symptoms in mice inoculated with RVΔP-MERS/S1. Moreover, virus-specific neutralizing antibodies against both MERS-CoV and RV were induced in mice inoculated intraperitoneally with RVΔP-MERS/S1. These findings indicate that RVΔP-MERS/S1 is a promising and safe bivalent-vaccine candidate against both MERS-CoV and RV.


title: Case Report: One Case of Coronavirus Desease 2019(COVID-19) in Patient Co-nfected by HIV With a Low CD4+ T Cell Count

text: Abstract The ongoing outbreak of COVID-19 that began in Wuhan, China has become an emergency of international concern When thousands of peolple were infected around the world.We report a case infected by SARS-Cov-2 and HIV simultaneously,which showed a longer course of disease and slower generation of specific antibody. This case highlights the coinfection of SARS-Cov-2 and HIV may impaire the immune system worse.


title: Hepatitis E virus (HEV): Molecular cloning and sequencing of the full-length viral genome

text: Abstract We have recently described the cloning of a portion of the hepatitis E virus (HEV) and confirmed its etiologic association with enterically transmitted (waterborne, epidemic) non-A, non-B hepatitis. The virus consists of a single-stranded, positive-sense RNA genome of approximately 7.5 kb, with a polyadenylated 3' end. We now report on the cloning and nucleotide sequencing of an overlapping, contiguous set of cDNA clones representing the entire genome of the HEV Burma strain [HEV(B)]. The largest open reading frame extends approximately 5 kb from the Fend and contains the RNA-directed RNA polymerase and nucleoside triphosphate binding motifs. The second major open reading frame (ORF2) begins 37 by downstream of the first and extends approximately 2 kb to the termination codon present 65 by from the 3' terminal stretch of poly(A) residues. ORF2 contains a consensus signal peptide sequence at its amino terminus and a capsid-like region with a high content of basic amino acids similar to that seen with other virus capsid proteins. A third open reading frame partially overlaps the first and second and encompasses only 369 bp. In addition to the 7.5-kb full-length genomic transcript, two subgenomic polyadenylated messages of approximately 3.7 and 2.0 kb were detected in infected liver using a probe from the 3' third of the genome. The genomic organization of the virus is consistent with the Fend encoding nonstructural and the 3' end encoding the viral structural gene(s). The expression strategy of the virus involves the use of three different open reading frames and at least three different transcripts. HEV was previously determined to be a nonenveloped particle with a diameter of 27–34 nm. These findings on the genetic organization and expression strategy of HEV suggest that it is the prototype human pathogen for a new class of RNA virus or perhaps a separate genus within the Caliciviridae family