title: A Peptide-based Magnetic Chemiluminescence Enzyme Immunoassay for Serological Diagnosis of Corona Virus Disease 2019 (COVID-19)

text: A respiratory illness has been spreading rapidly in China, since its outbreak in Wuhan city, Hubei province in December 2019. The illness was caused by a novel coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Clinical manifestations related to SARS-CoV-2 infection ranged from no symptom to fatal pneumonia. World Health Organization (WHO) named the diseases associated with SARS-CoV-2 infection as COVID-19. Real time RT-PCR is the only laboratory test available till now to confirm the infection. However, the accuracy of real time RT-PCR depends on many factors, including sampling location and of methods, quality of RNA extraction and training of operators etc. Variations in these factors might significantly lower the sensitivity of the detection. We developed a peptide-based luminescent immunoassay to detect IgG and IgM. Cut-off value of this assay was determined by the detection of 200 healthy sera and 167 sera from patients infected with other pathogens than SARS-CoV-2. To evaluate the performance of this assay, we detected IgG and IgM in the 276 sera from confirmed patients. The positive rate of IgG and IgM were 71.4% (197/276) and 57.2% (158/276) respectively. By combining with real time RT-PCR detection, this assay might help to enhance the accuracy of diagnosis of SARS-CoV-2 infection.


The COVID-19 Pandemic Crisis: The Loss and Trauma Event of Our Time


title: The mental health impact of the covid-19 pandemic onhealthcare workers, and interventions to help them: a rapid systematic review

text: Background: The covid-19 pandemic has heavily burdened, and in some cases overwhelmed, healthcare systems throughout the world. Healthcare workers are not only at heightened risk of infection, but also of adverse mental health outcomes. Identification of organizational, collegial and individual risk and resilience factors impacting the mental health of healthcare workers are needed to inform preparedness planning and sustainable response. Methods: We performed a rapid systematic review to identify, assess and summarize available research on the mental health impact of the covid-19 pandemic on healthcare workers. On 11 May 2020, we utilized the Norwegian Institute of Public Health's Live map of covid-19 evidence, the visualization of a database of 20,738 screened studies, to identify studies for inclusion. We included studies reporting on any type of mental health outcome in any type of healthcare workers during the pandemic. We described interventions reported by the studies, and narratively summarized mental health-related outcomes, as study heterogeneity precluded meta-analysis. We assessed study quality using design-specific instruments. Results: We included 59 studies, reporting on a total of 54,707 healthcare workers. The prevalence of general psychological distress across the studies ranged from 7-97% (median 37%), anxiety 9-90% (median 24%), depression 5-51% (median 21%), and sleeping problems 34-65% (median 37%). Seven studies reported on implementing mental health interventions, and most focused on individual symptom reduction, but none reported on effects of the interventions. In most studies, healthcare workers reported low interest in and use of professional help, and greater reliance on social support and contact with family and friends. Exposure to covid-19 was the most commonly reported correlate of mental health problems, followed by female gender, and worry about infection or about infecting others. Social support correlated with less mental health problems. Discussion: Healthcare workers in a variety of fields, positions, and exposure risks are reporting anxiety, depression, sleep problems, and distress during the covid-19 pandemic, but most studies do not report comparative data on mental health symptoms. before the pandemic. There seems to be a mismatch between risk factors for adverse mental health outcomes among healthcare workers in the current pandemic and their needs and preferences, and the individual psychopathology focus of current interventions. Efforts to help healthcare workers sustain healthy relationships to colleagues, family and friends over time may be paramount to safeguard what is already an important source of support during the prolonged crisis. Expanding interventions' focus to incorporate organizational, collegial and family factors to support healthcare workers responding to the pandemic could improve acceptability and efficacy of interventions. Other: The protocol for this review is available online. No funding was received.


title: Estimating the state of the Covid-19 epidemic in France using a non-Markovian model

text: In this paper, we use a deterministic non-Markovian epidemic model to estimate the state of the Covid-19 epidemic in France. This model allows us to consider realistic distributions for the exposed and infectious periods in a SEIR model, contrary to standard ODE models which only consider exponentially distributed exposed and infectious periods. We present theoretical results linking the (unobserved) parameters of the model to various quantities which are more easily measured during the early stages of an epidemic. We also stress the main quantitative differences between the non-Markovian and the Markovian (ODE) model. We then apply these results to estimate the state of the Covid-19 epidemic in France by analyzing three regions: the Paris region, the northeast regions and the rest of the country, based on current knowledge on the infection fatality ratio and the exposed and infectious periods distributions for Covid-19. Our analysis is based on the hospital data published daily by Sante Publique France (daily hospital admissions, intensive care unit admissions and hospital deaths).


title: REGIONAL DETERMINANTS OF THE EXPANSION OF COVID-19 IN BRAZIL

text: Objective: This study investigates the regional differences in the occurrence of COVID-19 in Brazil and its relationship with climatic and demographic factors, for this, using data about identified cases of COVID-19 on Brazil from February 26 to April 04, 2020. Methods: A model using the Polynomial Regression with cubic adjustments of the number of days of contagion, demographic density, city population and climatic factors was designed to explain the spread of COVID-19 in Brazil. Main results: It was evidenced that temperature variation maintains a relationship with the reduction in the number of cases of COVID-19, but on a very small scale. With a simulation of 30 days of contagion, a variation of -0.9% was found for each increase of 1 C. Conclusion: Temperature, despite being an intervening factor in the variation in the number of COVID-19 cases, has a reduced magnitude effect. Cities with higher temperatures do not necessarily it is more protected from the SARS-CoV-2 than those with lower temperatures, however, strong statistical significance was found, this relationship deserves to be investigated in other tests with longer time series, wide and with especially non-linear data adjustments.


title: Shotgun proteomics of SARS-CoV-2 infected cells and its application to the optimisation of whole viral particle antigen production for vaccines

text: Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has resulted in a pandemic and continues to spread quickly around the globe. Currently, no effective vaccine is available to prevent COVID-19 and an intense global development activity is in progress. In this context, the different technology platforms face several challenges resulting from the involvement of a new virus still not fully characterised. Finding of the right conditions for virus amplification for the development of vaccines based on inactivated or attenuated whole viral particles is among them. Here, we describe the establishment of a workflow based on shotgun tandem mass spectrometry data to guide the optimisation of the conditions for viral amplification. In parallel, we analysed the dynamic of the host cell proteome following SARS-CoV-2 infection providing a global overview of biological processes modulated by the virus and that could be further explored to identify drug targets to address the pandemic.


title: Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories

text: The pandemic of SARS coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a dataset of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean 5.5-9.5 nucleotide differences from each other, commensurate with a mid-range coronavirus substitution rate of 3×10−4 substitutions/site/year. Almost half of sequence changes were C->U transitions with an 8-fold base frequency normalised directional asymmetry between C->U and U->C substitutions. Elevated ratios were observed in other recently emerged coronaviruses (SARS-CoV and MERS-CoV) and to a decreasing degree in other human coronaviruses (HCoV-NL63, -OC43, -229E and -HKU1) proportionate to their increasing divergence. C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5’U/A and 3’U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Marked base asymmetries observed in non-pandemic human coronaviruses (U>>A>G>>C) and low G+C contents may represent long term effects of prolonged C->U hypermutation in their hosts. Importance The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. Repeated cycles of mutation and reversion in favoured mutational hotspots and the widespread occurrence of amino acid changes with no adaptive value for the virus represents a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks that are typically used in molecular epidemiology investigations.


title: Reassessing the quality of sea-ice deformation estimates derived from the RADARSAT Geophysical ProcessorSystem and its impact on the spatio-temporal scaling statistics

text: We reassess the trajectory tracking errors inherent to the Lagrangian deformation estimates with a new propagation of uncertainty derivation and show that previous formulations applied to deformation estimates from the RADARSAT Geophysical Processor System (RGPS) were either too low due to a simplistic formulation, or too high due to incorrect assumptions in the derivation. We show that when the resulting signal-to-noise ratios are used to discriminate the deformation estimates based on their quality, as done for buoy records, the spatio-temporal scaling exponents for the mean total deformation rate increase, especially at smaller scale, such that a space-time coupling of the scaling $-$ which is otherwise absent $-$ emerges from the RGPS deformation data set, in accord with previous analyses performed with buoy observations. We also show that the pre-processing method used to reduce the effects of irregular sampling of the Lagrangian deformation fields can significantly impact the value of the deformation statistics and could possibly explain part of previous discrepancies between deformation statistics obtained with buoy records and large-scale SAR imagery. Specifically, we show that spurious lines of deformation appear when interpolating RGPS trajectories presenting temporal sampling inconsistencies. In the context of using observed sea-ice deformation statistics to constrain and improve the performance of sea-ice models, high confidence in the observed deformation field statistics is necessary. Using appropriate, well-documented, methods to derive the set of statistics to be reproduced by models therefore becomes crucial.


title: Overhauling a faulty control in the CDC-recommended SARS-CoV-2 RT-PCR test panel

text: To battle the COVID-19 pandemic, widespread testing for the presence of the SARS-CoV-2 virus is worldwide being employed by specific real-time RT-PCR (rRT-PCR) of viral RNA. The CDC has issued a recommended panel of PCR-based test sets that entail several primer/probe sets that target the SARS-CoV-2 N-gene, but also one that targets the human RNase P gene (h-RP) as a positive control for RNA extraction and/or reverse-transcription (RT) efficacy. We discovered that the CDC-recommended h-RP primer/probe set has a faulty design, because both PCR primers are located in the same exon, which allows for unwanted PCR-amplification of background genomic DNA (gDNA). By removing RNA from nose-swab samples by an RNase treatment, we showed that the presence of gDNA in samples resulted in false-positive signals for the h-RP test control. This is rather serious, because it could lead to false-negative test outcomes, since the CDC interpretation of an absent SARS-CoV-2 rRT-PCR signal plus a positive h-RP rRT-PCR signal is interpreted as “2019-nCoV not detected”, whereas a false-positive h-RP rRT-PCR signal resulting from amplification of gDNA should be interpreted as “Invalid Result” and the procedure should be repeated. In order to overhaul the faulty h-RP rRT-PCR primer/probe set with minimal modification, we designed and tested several new h-RP reverse primers. Replacement of the CDC-recommended PCR reverse primer with our selected exon-exon junction reverse primer corrected the problem of false-positive results with this important SARS-CoV-2 RT-PCR test control and thus eliminated the problem of potential false-negative COVID-19 diagnoses.


title: Extended SIR Prediction of the Epidemics Trend of COVID-19 in Italy and Compared With Hunan, China

text: Background: Coronavirus Disease 2019 (COVID-19) is currently a global public health threat. Outside of China, Italy is one of the countries suffering the most with the COVID-19 epidemic. It is important to predict the epidemic trend of the COVID-19 epidemic in Italy to help develop public health strategies. Methods: We used time-series data of COVID-19 from Jan 22 2020 to Apr 02 2020. An infectious disease dynamic extended susceptible-infected-removed (eSIR) model, which covers the effects of different intervention measures in dissimilar periods, was applied to estimate the epidemic trend in Italy. The basic reproductive number was estimated using Markov Chain Monte Carlo methods and presented using the resulting posterior mean and 95% credible interval (CI). Hunan, with a similar total population number to Italy, was used as a comparative item. Results: In the eSIR model, we estimated that the mean of basic reproductive number for COVID-19 was 4.34 (95% CI, 3.04–6.00) in Italy and 3.16 (95% CI, 1.73–5.25) in Hunan. There would be a total of 182 051 infected cases (95%CI:116 114–274 378) under the current country blockade and the endpoint would be Aug 05 in Italy. Conclusion: Italy's current strict measures can efficaciously prevent the further spread of COVID-19 and should be maintained. Necessary strict public health measures should be implemented as soon as possible in other European countries with a high number of COVID-19 cases. The most effective strategy needs to be confirmed in further studies.


title: Elevated expression of ACE2 in tumor-adjacent normal tissues of cancer patients

text: The rapidly developing COVID-19 pandemic has raised a concern that cancer patients may have increased susceptibility to SARS-CoV-2 infection. This discussion has mostly focused on therapy-induced immune suppression. Here, we examined the expression patterns of ACE2, the receptor through which SARX-CoV2 enters human cells, and found that ACE2 mRNA levels are elevated in tumor-adjacent normal tissues of cancer patients, including in normal-adjacent lung tissues of lung cancer patients. These observations raise the possibility that the elevated COVID-19 risk of cancer patients may not be limited to those undergoing immune-suppressing treatment.


title: Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence

text: Background COVID-19 is a disease with global public health emergency that have shook the world since its’ first detection in China in December, 2019. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is the pathogen responsible behind this pandemic. The lethality of different viral strains is found to vary in different geographical locations but the molecular mechanism is yet to be known. Methods Available data of whole genome sequencing of different viral strains published by different countries were retrieved and then analysed using Multiple Sequence Alignment and Pair-wise Sequence Alignment leading to Phylogenetic tree construction. Each location and the corresponding genetic variations were screened in depth. Then the variations are analysed at protein level giving special emphasis on Non Synonymous amino acid substitutions. The fatality rates in different countries were matched against the mutation number, rarity of the nucleotide alterations and functional impact of the Non Synonymous changes at protein level, separately and in combination. Findings All the viral strains have been found to evolve from the viral strain of Taiwan (MT192759) which is 100% identical with the ancestor SARS-CoV-2 sequences of Wuhan (NC 045512.2; submitted on 5th Jan, 2020). Transition from C to T (C>T) is the most frequent mutation in this viral genome and mutations A>T, G>A, T>A are the rarest ones, found in countries with maximum fatality rate i.e Italy, Spain and Sweden. 20 Non Synonymous mutations are located in viral genome spanning Orf1ab polyprotein, Surface glycoprotein, Nucleocapsid protein etc. The functional effect on the structure and function of the protein can favourably or unfavourably interact with the host body. Interpretation The fatality outcome depends on three important factors (a) number of mutation (b) rarity of the allelic variation and (c) functional consequence of the mutation at protein level. The molecular divergence, evolved from the ancestral strain (S) lead to extremely lethal (E), lethal(L) and non lethal (N) strains with the involvement of an Intermediate strain(I).


title: Finish machining of Ti6Al4V SLM components under consideration of thin walls and support structure removal

text: Abstract Using additive manufacturing (AM) technologies such as powder bed based selective laser melting, it is possible to realize new bionic designs for Ti6Al4V aerospace components, thus significantly reducing weight. With these technologies, the goals of reducing emissions in the aviation industry can be achieved while passenger numbers are growing at the same time. In order to fulfill the quality requirements of the components, the AM process chain includes many further process steps in addition to melting, such as heat treatment. Furthermore, the functional surfaces must be machined and the support structures removed. These are essential for selective laser melting. The paper shows how the deflection of the workpiece can be minimized by milling thin-walled functional surfaces using a clamping device with support points. This increases the geometric accuracy considerably. Finally, the paper shows the results for milling support structures. The design of the support structure has a high effect on the machining behavior. Finally, results are presented that show the influence of different milling strategies on the surface quality of AM components, considering the support structures.


title: A consideration of publication-derived immune-related associations in Coronavirus and related lung damaging diseases

text: The severe acute respiratory syndrome virus SARS-CoV-2, a close relative of the SARS-CoV virus, is the cause of recent COVID-19 pandemic affecting, to date, over a 2 million individuals across the globe and demonstrating relatively high rates of infection and mortality. A third virus, the H5N1, responsible for avian influenza, has caused infection with some clinical similarities to those in COVID-19 infections. Cytokines, small proteins that modulate immune responses, have been directly implicated in some of the severe responses seen in COVID-19 patients, e.g. cytokine storms. Understanding the immune processes related to COVID-19, and other similar infections, could help identify diagnostic markers and therapeutic targets. Here we examine data of cytokine, immune cell types, and disease associations captured from biomedical literature associated with coronavirus, SARS, and H5N1 influenza, with the objective of identifying potentially useful relationships and areas for future research. Cytokine and cell-type associations captured from MeSH terms linked to thousands of PubMed abstracts, has identified differing patterns of associations between the three corpuses of abstracts (coronavirus, SARS, or H5N1 influenza). Clustering of cytokine-disease co-occurrences in the context of coronavirus has identified compelling clusters of co-morbidities and symptoms, some of which already known to be linked to COVID-19. Finally, network analysis identified sub-networks of cytokines and immune cell types associated with different manifestations, co-morbidities and symptoms of coronavirus, SARS, and H5N1. Systematic review of research in medicine is essential to facilitate evidence-based choices about health interventions. In a fast moving pandemic the approach taken here will identify trends and enable rapid comparison to the literature of related diseases.


title: Polymeric Pathogen-like Particles-Based Combination Adjuvants Elicit Potent Mucosal T Cell Immunity to Influenza A Virus

text: Eliciting durable and protective T cell-mediated immunity in the respiratory mucosa remains a significant challenge. Polylactic-co-glycolic acid (PLGA)-based cationic pathogen-like particles (PLPs) loaded with TLR agonists mimic biophysical properties of microbes and hence, simulate pathogen-pattern recognition receptor interactions to safely and effectively stimulate innate immune responses. We generated micro particle PLPs loaded with TLR4 (glucopyranosyl lipid adjuvant, GLA) or TLR9 (CpG) agonists, and formulated them with and without a mucosal delivery enhancing carbomer-based nanoemulsion adjuvant (ADJ). These adjuvants delivered intranasally to mice elicited high numbers of influenza nucleoprotein (NP)-specific CD8+/ CD4+ effector and tissue-resident memory T cells (TRMs) in lungs and airways. PLPs delivering TLR4 versus TLR9 agonists drove phenotypically and functionally distinct populations of effector and memory T cells. While PLPs loaded with CpG or GLA provided immunity, combining the adjuvanticity of PLP-GLA and ADJ synergistically enhanced the development of airway and lung TRMs and protective immunity to pathogenic influenza A virus. Further, balanced CD8 (Tc1/Tc17) and CD4 (Th1/Th17) recall responses were linked to effective influenza virus control in the lungs. These studies provide mechanistic insights into vaccine-induced T cell immunity in the respiratory tract and pave the way for the development of a universal influenza vaccine.


title: A CRISPR-Cas12a-based specific enhancer for more sensitive detection of SARS-CoV-2 infection

text: High Ct-values falling in the grey zone are frequently encountered in SARS-CoV-2 detection by real-time reverse transcription PCR (rRT-PCR) and have brought urgent challenges in diagnosis of samples with low viral load. Based on the single-stranded DNA reporter trans-cleavage activity by Cas12a upon target DNA recognition, we create a Specific Enhancer for detection of PCR-amplified Nucleic Acids (SENA) to confirm SARS-CoV-2 detection through specifically targeting its rRT-PCR amplicons. SENA is highly sensitive, with its limit of detection being at least 2 copies/reaction lower than that of the corresponding rRT-PCR, and highly specific, which identifies both false-negative and false-positive cases in clinic applications. SENA provides effective confirmation for nucleic acid amplification-based molecular diagnosis, and may immediately eliminate the uncertainty problems of rRT-PCR in SARS-CoV-2 clinic detection.


title: Early impact of the COVID-19 pandemic and social distancing measures on routine childhood vaccinations in England, January to April 2020

text: Electronic health records were used to assess the early impact of COVID-19 on routine childhood vaccination in England to 26 April 2020. MMR vaccination counts fell from February 2020, and in the three weeks after introduction of social distancing measures were 19.8% lower (95% CI -20.7 to -18.9%) than the same period in 2019, before improving in mid-April. A gradual decline in hexavalent vaccination counts throughout 2020 was not accentuated on introduction of social distancing.


title: Mental health outcomes and associations during the coronavirus disease 2019 pandemic: A cross-sectional survey of the US general population

text: Pandemic coronavirus disease 2019 (COVID-19) may lead to significant mental health stresses, potentially with modifiable risk factors. To determine the presence of and magnitude of associations between baseline associations and anxiety and depression in the US general population, we performed an internet-based cross-sectional survey of an age-, sex-, and race- stratified representative sample from the US general population. Degrees of anxiety, depression, and loneliness were assessed using the 7-item Generalized Anxiety Disorder scale (GAD-7), the 9-item Patient Health Questionnaire (PHQ-9), and the 8-item UCLA Loneliness Scale, respectively. Unadjusted and multivariable logistic regression analyses were performed to determine associations with baseline demographic characteristics. A total of 1,005 finished surveys were returned of the 1,020 started, yielding a completion rate of 98.5% in the survey panel. The mean (SD) age of respondents was 45 (16), and 494 (48.8%) were male. Baseline demographic data were similar between those that were (n=663, 66.2%) and were not (n=339, 33.8%) under a shelter in place/ stay at home order, with the exception of sex and geographic location. Overall, 264 subjects (26.8%) met criteria for an anxiety disorder based on a GAD-7 cutoff of 10; a cutoff of 7 yielded 416 subjects (41.4%) meeting clinical criteria for anxiety. On multivariable analysis, male sex (OR 0.65, 95% CI [0.49, 0.87]) and living in a larger home (OR 0.46, 95% CI [0.24, 0.88]) were associated with a decreased odds of meeting anxiety criteria. Rural location (OR 1.39, 95% CI [1.03, 1.89]), loneliness (OR 4.92, 95% CI [3.18, 7.62]), and history of hospitalization (OR 2.04, 95% CI [1.38, 3.03]), were associated with increased odds of meeting anxiety criteria. 232 subjects (23.6%) met criteria for clinical depression. On multivariable analysis, male sex (OR 0.71, 95% CI [0.53, 0.95]), increased time outdoors (OR 0.51, 95% CI [0.29, 0.92]), and living in a larger home (OR 0.35, 95% CI [0.18, 0.69]), were associated with decreased odds of meeting depression criteria. Having lost a job (OR 1.64, 95% CI [1.05, 2.54]), loneliness (OR 10.42, 95% CI [6.26, 17.36]), and history of hospitalization (OR 2.42, 95% CI [1.62, 3.62]), were associated with an increased odds of meeting depression criteria. Income, media consumption, and religiosity were not associated with mental health outcomes. Anxiety and depression are common in the US general population in the context of the COVID-19 pandemic, and are associated with potentially modifiable factors.


title: The effect of the COVID-19 induced lockdown on nutrition, health and lifestyle patterns among adults in Zimbabwe

text: Background: The 2019 coronavirus disease (COVID-19) is a global public health nightmare resulting in lockdowns, associated diet and lifestyle changes and constraint public health delivery. Objective: To investigate the impacts of the COVID-19 induced lockdown in Zimbabwe on nutrition, physical activity and lifestyle patterns among Zimbabwean population aged [≥]18years. Methods: A cross-sectional online survey was conducted using a structured questionnaire to collect information on demographics (age, gender, place of residence, current employment), food system dimensions, diet and physical activity patterns, stress and anxiety, body image perceptions, lifestyle behaviours like smoking, alcohol intake, screen time, and ease of access to health services. Electronic informed consent was obtained from all participants prior to completing the survey. Results: The majority of the participants were between the ages of 31-40 years, were female (63.0%) and had tertiary education (91.3%). The lockdown resulted in increase in food prices (94.8%) and decrease in availability of nutritious foods (64%). Most (62.5%) of the participants reported a reduction in their physical activity levels. The prevalence of Generalised Anxiety Disorder (GAD) was 40.4% and mostly affecting females [63.5%, P=0.909), 31-40 years age group (49.6%, P=0.886). Based on the BMI-based Silhouette Matching Test (BMI-SMT) 44.5% gained weight, 24.3% lost weight and 31.2% did not have weight change. The paired samples T test showed that there was a significant increase in perceived body weight (P<0.001). More than half (59.6%) reported having difficulties accessing drugs and medication and 37.8% growth monitoring services. Conclusions: The lockdown period was associated with increase in food prizes, decrease in dietary diversification, elevated stress, disrupted diet and consumption patterns. There was low levels of physical activity and perceived weight gained during the lockdown period. However, there are still lots on unknowns concerning the COVID-19 pandemic future studies with larger population are required.


title: COVID-19 Tragic Pandemic: Concerns over Unintentional “Directed Accelerated Evolution” of Novel Coronavirus (SARS-CoV-2) and Introducing a Modified Treatment Method for ARDS

text: Global health authorities are trying to work out the current status of the novel coronavirus (COVID-19) outbreak and explore methods to reduce the rate of its transmission to healthy individuals. In this viewpoint we provide insights concerning how health care professionals can unintentionally shift the novel coronavirus type to more drug-resistant forms. It is worth noting that viruses usually have different sensitivities to physical and chemical damaging agents such antiviral drugs, UV and heat ranging from extremely sensitive (ES) to extremely resistant (ER) based on a bell-shaped curve. Given this consideration, the widespread infection of people with such ER viruses would be a real disaster. Here, we introduce a modified treatment method for COVID-19-associated pneumonia. In this proposed method, COVID-19 patients will receive a single dose of 100, 180 or 250 mSv X-ray radiation that is less than the maximum annual radiation dose of the residents of high background radiation areas of Ramsar that is up to 260 mSv. In contrast with antiviral drugs, a single dose of either 100, 180 or 250 mSv of low LET X-rays cannot exert a significant selective pressure on the novel coronavirus (SARS-CoV-2) and hence does not lead to directed accelerated evolution of these viruses. Moreover, Low Dose Radiation (LDR) has the capacity of modulating excessive inflammatory responses, regulating lymphocyte counts, and controling bacterial co-infections in patients with COVID-19.


title: Assessment of the MERS-CoV epidemic situation in the Middle East region

text: The appearance of a novel coronavirus named Middle East (ME) Respiratory Syndrome Coronavirus (MERS-CoV) has raised global public health concerns regarding the current situation and its future evolution. Here we propose an integrative maximum likelihood analysis of both cluster data in the ME region and importations in Europe to assess transmission scenario and incidence of sporadic infections. Our approach is based on a spatial-transmission model integrating mobility data worldwide and allows for variations in the zoonotic/environmental transmission and underascertainment. Maximum likelihood estimates for the ME region indicate the occurrence of a subcritical epidemic (R=0.50, 95% confidence interval (CI) 0.30-0.77) associated with a 0.28 (95% CI 0.12-0.85) daily rate of sporadic introductions. Infections in the region appear to be mainly dominated by zoonotic/environmental transmissions, with possible underascertainment (95% CI of estimated to observed sporadic cases in the range 1.03-7.32). No time evolution of the situation emerges. Analyses of flight passenger data from the region indicate areas at high risk of importation. While dismissing an immediate threat for global health security, this analysis provides a baseline scenario for future reference and updates, suggests reinforced surveillance to limit underascertainment, and calls for increased alertness in high-risk areas worldwide.


title: Introductions and early spread of SARS-CoV-2 in the New York City area

text: New York City (NYC) has emerged as one of the epicenters of the current SARS-CoV2 pandemic. To identify the early events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus causing COVID19 in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV2 genomes indicates multiple, independent but isolated introductions mainly from Europe and other parts of the United States. Moreover, we find evidence for community transmission of SARS-CoV2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city.


title: Unraveling the Myths of R0 in Controlling the Dynamics of COVID-19 Outbreak: a Modelling Perspective

text: COVID-19 is an emerging and rapidly evolving pandemic around the world, which causes severe acute respiratory syndrome and results in substantial morbidity and mortality. To examine the transmission dynamics of COVID-19 and its interactions with some exogenous factors such as limited medical resources and false detection problems, we employ a simple epidemiological model and analyse this system using modelling and dynamical systems techniques. We discover some contrasting findings with respect to the observations of basic reproduction number, and we investigate how the issues of limited medical resources and false detection problems affect the COVID-19 pandemic outbreak.


title: Informing Homemade Emergency Facemask Design: The Ability of Common Fabrics to Filter Ultrafine Particles

text: Objectives: To examine the ability of fabrics which might be used to create homemade face masks to filter out ultrafine (smaller than 1m in diameter) particles. Method: Twenty commonly available fabrics and materials were evaluated for their ability to reduce air concentrations of ultrafine particles. Further assessment was made on the filtration ability of select fabrics while damp and of fabric combinations which might be used to construct homemade masks. Results: Single fabric layers blocked a range of ultrafine particles. When fabrics were layered, significantly more ultrafine particles were filtered. Several fabric combinations were successful in removing similar amounts of ultrafine particles when compared to an N95 mask and surgical mask. Conclusions: The current coronavirus pandemic has left many communities without access to commercial facemasks. Our findings suggest that face masks made from layered common fabric can help filter ultrafine particles and provide some protection for the wearer when commercial facemasks are unavailable.


title: Pitting the Gumbel and logistic growth models against one another to model COVID-19 spread

text: In this paper, we investigate briefly the appropriateness of the widely used logistic growth curve modeling with focus on COVID-19 spread, from a data-driven perspective. Specifically, we suggest the Gumbel growth model for behaviour of COVID-19 cases in European countries in addition to the United States of America (US), for better detecting the growth and prediction. We provide a suitable fit and predict the growth of cases for some selected countries as illustration. Our contribution will stimulate the correct growth spread modeling for this pandemic outbreak.


title: Behavior of susceptible-vaccinated--infected--recovered epidemics with diversity in the infection rate of the individuals

text: We study a susceptible-vaccinated--infected--recovered (SVIR) epidemic-spreading model with diversity of infection rate of the individuals. By means of analytical arguments as well as extensive computer simulations, we demonstrate that the heterogeneity in infection rate can either impede or accelerate the epidemic spreading, which depends on the amount of vaccinated individuals introduced in the population as well as the contact pattern among the individuals. Remarkably, as long as the individuals with different capability of acquiring the disease interact with unequal frequency, there always exist a cross point for the fraction of vaccinated, below which the diversity of infection rate hinders the epidemic spreading and above which expedites it. The overall results are robust to the SVIR dynamics defined on different population models; the possible applications of the results are discussed.


title: In-host Modelling of COVID-19 Kinetics in Humans

text: COVID-19 pandemic has underlined the impact of emergent pathogens as a major threat for human health. The development of quantitative approaches to advance comprehension of the current outbreak is urgently needed to tackle this severe disease. In this work, several mathematical models are proposed to represent COVID-19 dynamics in infected patients. Considering different starting times of infection, parameters sets that represent infectivity of COVID-19 are computed and compared with other viral infections that can also cause pandemics. Based on the target cell model, COVID-19 infecting time between susceptible cells (mean of 30 days approximately) is much slower than those reported for Ebola (about 3 times slower) and influenza (60 times slower). The within-host reproductive number for COVID-19 is consistent to the values of influenza infection (1.7-5.35). The best model to fit the data was including immune responses, which suggest a slow cell response peaking between 5 to 10 days post onset of symptoms. The model with eclipse phase, time in a latent phase before becoming productively infected cells, was not supported. Interestingly, both, the target cell model and the model with immune responses, predict that virus may replicate very slowly in the first days after infection, and it could be below detection levels during the first 4 days post infection. A quantitative comprehension of COVID-19 dynamics and the estimation of standard parameters of viral infections is the key contribution of this pioneering work.


title: Estimation of local novel coronavirus (COVID-19) cases in Wuhan, China from off-site reported cases and population flow data from different sources

text: Backgrounds: In December 2019, a novel coronavirus (COVID-19) pneumonia hit Wuhan, Hubei Province, China and spread to the rest of China and overseas. The emergence of this virus coincided with the Spring Festival Travel Rush in China. It is possible to estimate total number of cases of COVID-19 in Wuhan, by 23 January 2020, given the cases reported in other cities and population flow data between cities. Methods: We built a model to estimate the total number of cases in Wuhan by 23 January 2020, based on the number of cases detected outside Wuhan city in China, with the assumption that if the same screening effort used in other cities applied in Wuhan. We employed population flow data from different sources between Wuhan and other cities/regions by 23 January 2020. The number of total cases was determined by the maximum log likelihood estimation. Findings: From overall cities/regions data, we predicted 1326 (95% CI: 1177, 1484), 1151 (95% CI: 1018, 1292) and 5277 (95% CI: 4732, 5859) as total cases in Wuhan by 23 January 2020, based on different source of data from Changjiang Daily newspaper, Tencent, and Baidu. From separate cities/regions data, we estimated 1059 (95% CI: 918, 1209), 5214 (95% CI: 4659, 5808) as total cases in Wuhan in Wuhan by 23 January 2020, based on different sources of population flow data from Tencent and Baidu. Conclusion: Sources of population follow data and methods impact the estimates of local cases in Wuhan before city lock down. Keyword: COVID-19; mobility; pneumonia; transportation; outbreaks


title: 5.01 1,2,3-Triazoles

text: Rapid progress in the synthetic application of benzotriazole derivatives in the last 20 years has resulted in over 1000 scientific papers on the subject. This fact is reflected in Section 5.01.7, which involves almost a half of the volume of this chapter. The section is arranged according to hybridization of the C-α atom and atomic numbers of the atoms in positions β and γ to allow an easy access to the material of interest. Recent discovery of copper catalysis in [3+2] cycloadditions of azides to acetylenes, the so-called ‘click chemistry’, which boosted application of the 1,2,3-triazole derivatives, especially in medicinal chemistry, is presented in Section 5.01.9. From the point of view of practical applications, Section 5.01.11 is organized according to the number, position, and combination of the substituents at the aromatic rings. Another novel feature that has no precedence in the previous editions of Comprehensive Heterocyclic Chemistry is an addition of triazole and benzotriazole complexes with various transitions metals to Section 5.01.4.


title: Resilience in the face of uncertainty: early lessons from the COVID-19 pandemic

text: The transboundary dynamics of COVID-19 present an unprecedented test of organisational resilience. In the UK, the National Health Service (NHS), a talisman of collective fortitude against disease and illness, has struggled to cope with inadequate provision of virus tests, ventilators, and personal protective equipment needed to fight the pandemic. In this paper, we reflect on the historic dynamics and strategic priorities that have undermined the NHS’s attempts to navigate these troubled times. We invoke the organisational resilience literature to address ‘the good, the bad and the ugly’ of preparedness in readiness and response to the current pandemic. In particular, we draw on Meyer’s (1982) seminal work on ‘adaptation to jolts’, excavating current preparedness failings. We argue an overreliance on perceived efficiency benefits of ‘lean production’ and ‘just in time’ continuity planning superseded strategic redundancy and slack in the system. This strategic focus was not simply the result of a failure in foresight, but rather a failure to act adaptively on knowledge of the known threats and weaknesses spotlighted by earlier projections of an inevitable pandemic threat. In conclusion, we consider how the UK Government and NHS must now undergo a phase of ‘readjustment’ in Meyer’s terms, in light of these failings. We suggest that independent responsibility for national future preparedness should be handed to the NHS free from political interference. This would operate under the umbrella of a national emergency preparedness, resilience and response public body, enshrined in law, and similar in governance to the current Bank of England. This will help ensure that foresight is accompanied by durability and fortitude in safeguarding the UK against future pandemic threats.


title: Indoor transmission of SARS-CoV-2

text: Background: By early April 2020, the COVID-19 pandemic had infected nearly one million people and had spread to nearly all countries worldwide. It is essential to understand where and how SARS-CoV-2 is transmitted. Methods: Case reports were extracted from the local Municipal Health Commissions of 320 prefectural cities (municipalities) in China, not including Hubei province, between 4 January and 11 February 2020. We identified all outbreaks involving three or more cases and reviewed the major characteristics of the enclosed spaces in which the outbreaks were reported and associated indoor environmental issues. Results: Three hundred and eighteen outbreaks with three or more cases were identified, involving 1245 confirmed cases in 120 prefectural cities. We divided the venues in which the outbreaks occurred into six categories: homes, transport, food, entertainment, shopping, and miscellaneous. Among the identified outbreaks, 53.8% involved three cases, 26.4% involved four cases, and only 1.6% involved ten or more cases. Home outbreaks were the dominant category (254 of 318 outbreaks; 79.9%), followed by transport (108; 34.0%; note that many outbreaks involved more than one venue category). Most home outbreaks involved three to five cases. We identified only a single outbreak in an outdoor environment, which involved two cases. Conclusions: All identified outbreaks of three or more cases occurred in an indoor environment, which confirms that sharing indoor space is a major SARS-CoV-2 infection risk.


Understanding Trend of the Covid-19 Fatalities in India


title: AJN On the CoverWhere Are the Masks?

text: Shortages of vital PPE during the COVID-19 pandemic


title: Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing

text: Coronavirus Disease-2019 (COVID-19) is an infectious disease caused by the SARS-CoV-2 virus. It was first identified in Wuhan, China, and has since spread causing a global pandemic. Various studies have been performed to understand the molecular mechanisms of viral infection for predicting drug repurposing candidates. However, such information is spread across many publications and it is very time-consuming to access, integrate, explore, and exploit. We developed CoVex, the first interactive online platform for SARS-CoV-2 and SARS-CoV-1 host interactome exploration and drug (target) identification. CoVex integrates 1) experimentally validated virus-human protein interactions, 2) human protein-protein interactions and 3) drug-target interactions. The web interface allows user-friendly visual exploration of the virus-host interactome and implements systems medicine algorithms for network-based prediction of drugs. Thus, CoVex is an important resource, not only to understand the molecular mechanisms involved in SARS-CoV-2 and SARS-CoV-1 pathogenicity, but also in clinical research for the identification and prioritization of candidate therapeutics. We apply CoVex to investigate recent hypotheses on a systems biology level and to systematically explore the molecular mechanisms driving the virus life cycle. Furthermore, we extract and discuss drug repurposing candidates involved in these mechanisms. CoVex renders COVID-19 drug research systems-medicine-ready by giving the scientific community direct access to network medicine algorithms integrating virus-host-drug interactions. It is available at https://exbio.wzw.tum.de/covex/.


Post-COVID-19 Chinese domestic tourism market recovery: potential influence of traditional Chinese medicine on tourist behaviour


title: COVID-19: how can we support each other (and ourselves)?

text: The Chair of The National Hearing Voices Network (http://www.hearing-voices.org/HVN) prepared this document, on behalf of the HVN Board, to provide some sources of information and support for its members, and others, during the Covid-19 pandemic. At the request of the journal Editor (also a member of the HVN Board), the document is published here, verbatim, for Psychosis readers around the world. Although targeted at people in the UK who hear voices or see visions, much of the information is potentially also relevant for other people, including mental health professionals. Like HVN, neither the journal nor ISPS endorse or recommend specific mental health services or practitioners. We recognise that different things are helpful for different people. The document is published merely to increase the range of options for people to choose from if they feel the need for additional support or information. All at HVN, Psychosis and ISPS wish readers a safe passage though the current stormy waters, which, despite all the fears and losses, are providing us all with opportunities to take care of one another like many of us have never experienced before.


title: Strategies and Solutions for Team Sports Athletes in Isolation due to COVID-19

text: In December of 2019, there was an outbreak of a severe acute respiratory syndrome caused by the Coronavirus 2 (SARS-CoV-2 or COVID-19) in China. The virus rapidly spread into the whole World causing an unprecedented pandemic and forcing governments to impose a global quarantine, entering an extreme unknown situation. The organizational consequences of quarantine/isolation are: absence of organized training and competition, lack of communication among athletes and coaches, inability to move freely, lack of adequate sunlight exposure, inappropriate training conditions. Based on the current scientific, we strongly recommend encouraging the athlete to reset their mindset to understand quarantine as an opportunity for development, organizing appropriate guidance, educating and encourage athletes to apply appropriate preventive behavior and hygiene measures to promote immunity and ensuring good living isolation conditions. The athlete’s living space should be equipped with cardio and resistance training equipment (portable bicycle or rowing ergometer). Some forms of body mass resistance circuit-based training could promote aerobic adaptation. Sports skills training should be organized based on the athlete’s needs. Personalized conditioning training should be carried out with emphasis on neuromuscular performance. Athletes should also be educated about nutrition (Vitamin D and proteins) and hydration. Strategies should be developed to control body composition. Mental fatigue should be anticipated and mental controlled. Adequate methods of recovery should be provided. Daily monitoring should be established. This is an ideal situation in which to rethink personal life, understanding the situation, that can be promoted in these difficult times that affect practically the whole world.


title: Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCov literature

text: During the current century, each major coronavirus outbreak has triggered a quick and immediate surge of academic publications on this topic. The spike in research publications following the 2019 Novel Coronavirus (Covid-19) outbreak, however, has been like no other. The global crisis caused by the Covid-19 pandemic has mobilised scientific efforts in an unprecedented way. In less than five months, more than 12,000 research items have been indexed while the number increasing every day. With the crisis affecting all aspects of life, research on Covid-19 seems to have become a focal point of interest across many academic disciplines. Here, scientometric aspects of the Covid-19 literature are analysed and contrasted with those of the two previous major Coronavirus diseases, i.e. Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). The focus is on the co-occurrence of key-terms, bibliographic coupling and citation relations of journals and collaborations between countries. Certain recurring patterns across all three literatures were discovered. All three outbreaks have commonly generated three distinct and major cohort of studies: (i) studies linked to the public health response and epidemic control, (ii) studies associated with the chemical constitution of the virus and (iii) studies related to treatment, vaccine and clinical care. While studies affiliated with the category (i) seem to have been the first to emerge, they overall received least numbers of citations compared to those of the two other categories. Covid-19 studies seem to have been distributed across a broader variety of journals and subject areas. Clear links are observed between the geographical origins of each outbreak or the local geographical severity of each outbreak and the magnitude of research originated from regions. Covid-19 studies also display the involvement of authors from a broader variety of countries compared to SARS and MRS.


title: Optimal time frequency analysis for biological data - pyBOAT

text: Methods for the quantification of rhythmic biological signals have been essential for the discovery of function and design of biological oscillators. Advances in live measurements have allowed recordings of unprecedented resolution revealing a new world of complex heterogeneous oscillations with multiple noisy non-stationary features. However, our understanding of the underlying mechanisms regulating these oscillations has been lagging behind, partially due to the lack of simple tools to reliably quantify these complex non-stationary features. With this challenge in mind, we have developed pyBOAT, a Python-based fully automatic stand-alone software that integrates multiple steps of non-stationary oscillatory time series analysis into an easy-to-use graphical user interface. pyBOAT implements continuous wavelet analysis which is specifically designed to reveal time-dependent features. In this work we illustrate the advantages of our tool by analyzing complex non-stationary time-series profiles. Our approach integrates data-visualization, optimized sinc-filter detrending, amplitude envelope removal and a subsequent continuous-wavelet based time-frequency analysis. Finally, using analytical considerations and numerical simulations we discuss unexpected pitfalls in commonly used smoothing and detrending operations.


title: Immunological assays for SARS-CoV-2: an analysis of available commercial tests to measure antigen and antibodies

text: The rapid spread of SARS-CoV-2 coronavirus infection has led to the development of molecular and serologic tests in a short period of time. While tests such as RT-PCR have applications in the immediate diagnosis revealing the presence of the virus, serological tests can be used to determine previous exposure to the virus and complement acute diagnosis. Antibody production can occur as early as 5 days post-infection. Both IgM and IgG specific anti-SARS-COV-2 antibodies can be a useful tool to test faster and larger groups of individuals. The objective of this study was to carry out a review of the different serological tests offered to detect antigen or antibodies against SARS-CoV-2. This information should be useful for decision takers in different countries to choose a test according to their needs. Based on web pages that listed serological assays, we found 226 coming from 20 countries, the majority are indirect tests for specific antibodies detection (n 180) and use immunochromatography methods (n 110) with samples coming from blood-derived products (n 105). Measuring IgM/IgG at the same time (n 112) and a procedure time of <20 min (n 83) are the most common. The overall average sensitivity was 91.8% and specificity was 97%. Most of the tests are currently for in vitro diagnosis (IVD). This information gathered could change day by day due to the expedite process of production and emergency of authorization use.


title: Mental Health Impact of COVID-19: A global study of risk and resilience factors

text: This study anonymously screened 13,332 individuals worldwide for psychological symptoms related to Corona virus disease 2019 (COVID-19) pandemic from March 29th to April 14th, 2020. A total of n=12,817 responses were considered valid with responses from 12 featured countries and five WHO regions. Female gender, pre-existing psychiatric condition, and prior exposure to trauma were identified as notable riskfactors, whereas optimism, ability to share concerns with family and friends like usual,positive prediction about COVID-19, and daily exercise predicted fewer psychologicalsymptoms. These results could aid in dynamic optimization of mental health services during and following the COVID-19 pandemic.


title: Small interfering RNAs are highly effective inhibitors regarding Crimean-Congo hemorrhagic fever virus replication in vitro

text: Crimean-Congo hemorrhagic fever virus (CCHFV) is one of the prioritized diseases of World Health Organization, considering its potential to create a public health emergency and more importantly, the absence of efficacious drugs and/or vaccines regarding treatment. The highly lethal nature characteristic to CCHFV restricts research to BSL-4 laboratories, which complicates effective research and developmental strategies. In consideration of antiviral therapies, RNA interference can be used to suppress viral replication by targeting viral genes. RNA interference uses small interfering RNAs (siRNAs) to silence genes. The aim of our study was to design siRNAs that inhibit CCHFV replication and can serve as a basis for further antiviral therapies. A549 cells were infected with CCHFV after transfection with the siRNAs. Following 72 hours, nucleic acid from the supernatant was extracted for Droplet Digital PCR analysis. Among the investigated siRNAs we identified four effective candidates against all three segments of CCHF genome: one for the S and M segments, whilst two for the L segment. Consequently, blocking any segment of CCHFV leads to changes in the virus copy number that indicates an antiviral effect of the siRNAs in vitro. The most active siRNAs were demonstrated a specific inhibitory effect against CCHFV in a dose-dependent manner. In summary, we demonstrated the ability of specific siRNAs to inhibit CCHFV replication in vitro. This promising result can be used in future anti-CCHFV therapy developments.


title: Restoration of leukomonocyte counts is associated with viral clearance in COVID-19 hospitalized patients

text: Background: Viral clearance is one important indicator for the recovery of SARS-CoV-2 infected patients. Suboptimal T and B cell responses can delay viral clearance in MERS and SARS patients. The role of leukomonocytes in viral clearance of COVID-19 patients is not yet well defined.Methods: From January 26 to February 28, 2020, an observational study was launched at Zhongnan Hospital of Wuhan University, Wuhan, China. We enrolled 25 laboratory-confirmed COVID-19 patients, whose throat-swab specimens were tested positive for SARS-CoV-2 infection by qRT-PCR. We comprehensively analyzed clinical records, counts of lymphocyte subsets including CD3+, CD4+, CD8+ T cells, B cells and NK cells in the patients who successfully cleared SARS-CoV-2, and compared to those that failed to, after a standardized treatment of 8-14 days. Findings: In 25 enrolled COVID-19 patients, lymphopeniawas a common feature. After the treatment, 14 patients were tested negative for SARS-CoV-2. The patients that cleared the infection had restored the numbers of CD3+, CD4+, CD8+ T cellsand B cells as compared to the still viral RNA positive patients, while the recovered patients had a higher count of leukomonocytes. Conclusions: By comparison of leukomonocytes counts in COVID-19 patients at different stages of the disease, we found that CD3+, CD4+, CD8+ T cells and B cells appear to play important roles in viral clearance. The restoration of leukomonocytes counts from peripheral blood can be used as prognosis for the recovery of an COVID-19 infection. We propose that restoration of leukomonocytes counts can be added to the COVID-19 diagnostic guidanceas a criterion for releasing and discharging patients.


title: Interactions of SARS-CoV-2 infection with chronic obesity inflammation: a complex network phenomenon

text: Obesity is one of the biggest public health problems in the world, and its pathophysiological characteristics include chronic inflammation with an increase in various circulating inflammatory markers, such as acute inflammatory cytokines. Complications in the respiratory tract are related to bodily problems, which lead to a restriction of lung function due to reduced volume, inducing an increase in respiratory work. SARS-CoV-2 has a high potential for contamination by respiratory secretions and, therefore, obesity is one of the main risk factors for complications due to the association established between obesity, chronic inflammation and respiratory infection. The objective was to analyze the complex relationships between obesity and COVID-19 in a meta-analysis study using complex network modeling and the theoretical knockouts technique. Here, we identify and justify through a mathematical analysis the relationships between all the immunological agents added to the proposed immunological networks, considered as a simple evident interaction, relationship, influence, response, activation, based on our quantifiers. They performed the knockouts of all 52 vertices in the COVID-19 network and obesity - regardless of the environment, which would result in nonsense - and the COVID-19 infection network without considering obesity. The stationary flow vector (flow profile), for some knockouts of immunological interest in COVID-19 infections, was chosen IFNα, IL-6, IL-10, IL-17 and TNFα. This initial study pointed out the importance of chronic inflammation in the obese individual as an important factor in potentiating the disease caused by covid-19 and, in particular, the importance on IL-17.


title: Mobility trends provide a leading indicator of changes in SARS-CoV-2 transmission

text: Determining the impact of non-pharmaceutical interventions on transmission of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is paramount for the design and deployment of effective public health policies. Incorporating Apple Maps mobility data into an epidemiological model of daily deaths and hospitalizations allowed us to estimate an explicit relationship between human mobility and transmission in the United States. We find that reduced mobility explains a large decrease in the effective reproductive number attained by April 1st and further identify state-to-state variation in the inferred transmission-mobility relationship. These findings indicate that simply relaxing stay-at-home orders can rapidly lead to outbreaks exceeding the scale of transmission that has occurred to date. Our findings provide quantitative guidance on the impact policies must achieve against transmission to safely relax social distancing measures.


title: Impact of healthcare worker shift scheduling on workforce preservation during the COVID-19 pandemic

text: Background: As we contend with the massive SARS-CoV-2 pandemic, preventing infections among healthcare workers (HCW) and patients is critical for delivering care to patients admitted for other purposes, and many standard scheduling practices require reassessment. In most academic hospitals in the United States, inpatient rotations are designed to deliver optimal patient care by staggering rotations of attendings and house-staff, and much emphasis is placed on healthcare worker (HCW) burnout, yet during a pandemic preventing further infection is the single most important factor. Our purpose was to model various inpatient rotation schedules of physicians and nurses to determine patterns associated with optimal workforce preservation and lower nosocomial infections in settings in which personal protective equipment is imperfect or unavailable. Results: We employed Monte-Carlo simulations. Universal model parameters for COVID-19 included incubation period distribution and latent period distribution. Situation-dependent COVID-19 model parameters included pre-admission infection probability, team member infection probability, physician-to-patient, nurse-to-patient, patient-to-physician, patient-to-nurse, and HCW-to-HCW transmission probabilities, team member absence after symptom onset, daily SARS-CoV-2 exposure probability of team members (e.g. via exposure to other staff), length of admission after COVID-19 symptoms, and length of simulation time. Model parameters that varied by hospital setting and service type included average patient load per team, average patient hospitalization, and number of physicians and nurses on a team and on duty. The primary outcome measure was probability of team failure, defined as the likelihood that at some point there are insufficient attendings, house-staff or nurses to staff a fully functioning floor. In all our simulations, physician and nurse rotation lengths of 1-3 days led to higher team failure rates. Nursing shifts of 12 versus 8 hours and avoiding staggering of physician rotations decreased the chance of team failure. When the patient stay is short, the advantage of un-staggered rotations is consistent and universal. Conclusions: Simple changes in staff scheduling, such as longer nursing shifts, co-rotation of physicians and groups of nurses no more frequently than every 3 days results in improved workforce preservation. These workforce distancing changes are easy to implement.


title: Predictable county-level estimates of R0 for COVID-19 needed for public health planning in the USA

text: The basic reproduction number, R0, determines the rate of spread of a communicable disease and therefore gives fundamental information needed to plan public health interventions. Estimated R0 values are only useful, however, if they accurately predict the future potential rate of spread. Using mortality records, we estimated the rate of spread of COVID-19 among 160 counties and county-aggregates in the USA. Among-county variance in R0 estimates was explained by four factors: the timing of the county-level outbreak, population size, population density, and spatial location. The high predictability of R0 makes it possible to extend estimates to all counties in the lower 48 States. The predictability also makes the R0 estimates valuable guides for designing long-term public health policies for controlling COVID-19.


Canada and coronavirus: could have done better


title: Meningoencephalitis associated with COVID-19: A systematic review

text: Background and aims: With the growing number of COVID-19 cases in recent times, the varied range of presentations is progressively becoming an addressing issue among clinicians. A significant set of patients with extra pulmonary symptoms has been reported worldwide. Neurological involvement in the form of altered mental status, loss of consciousness in considerable amounts has drawn attention of physicians all across the globe. Here we venture out to summarise the clinical profile, investigations and radiological findings among patients with SARS-CoV-2 associated meningoencephalitis in the form of a systematic review, which may aid clinicians in early diagnosis and prognostic evaluation of the disease. Methodology: This review was carried out based on the existing PRISMA (Preferred Report for Systemic Review and Meta analyses) consensus statement. The data for this review was collected from four databases: Pubmed/Medline, NIH Litcovid, Embase and Cochrane library and Preprint servers up till 10th June, 2020. Search strategy comprised of a range of keywords from relevant medical subject headings which includes "SARS-COV-2", "COVID-19", "meningoencephalitis" etc. All peer reviewed, case control, case report, pre print articles satisfying our inclusion criteria were involved in the study. The inclusion prerequisites comprised of confirmed SARS-CoV-2 cases with neurological manifestations, previous cases of SARS-CoV, MERS-CoV with neurological involvement provided all the studies were published in English language. Quantitative data was expressed in mean+/-SD, while the qualitative date in percentages. Paired t test was used for analysing the data based on differences between mean and respective values with a p value of <0.05 considered to be statistically significant. Results: A total of 43 cases were involved from 24 studies after screening from databases and preprint servers, out of which 29 of them had completed investigation profile and were included in the final analysis. Clincial and Laboratory findings as well as neuroimaging findings (CT, MRI and MRS) revealed consistent presentations towards association of COVID-19 with meningoencephalitis. Epileptogenic pictures were also evident on EEG (electroencephalogram) findings. Conclusion: SARS-CoV-2 has been isolated from CSF as well as cerebrum of cases with meningoencephalitis depicting the natural tendency of the virus to invade the central nervous system. Speculations about retrograde olfactory transport or alternative haematogenous spread seem to be correlating with above findings. This review may raise the index of suspicion about COVID-19 among clinicians while attending patients with neurological manifestations.


title: Health Education for Parents During the COVID-19 OutbreakPublic Health Education for Parents During the Outbreak of COVID-19: A Rapid Review

text: Background: It is well-known that public health education plays a crucial role in the prevention and control of emerging infectious diseases, but how health providers should advise families and parents to obtain health education information is a challenging question. With COVID-19 (Coronavirus disease 2019) spreading around the world, this rapid review aims to answer that question and thus to promote evidence-based decision making in health education policy and practice. Methods: We systematically searched the literature on health education during COVID-19, SARS (severe acute respiratory syndrome) and MERS (middle east respiratory syndrome) epidemics in Medline (via PubMed), Cochrane Library, EMBASE, Web of Science, CBM (China Biology Medicine disc), CNKI (China National Knowledge Infrastructure), and Wanfang Data from their inception until March 31, 2020. The potential bias of the studies was assessed by Joanna Briggs Institute Prevalence Critical Appraisal Tool. Results: Of 1067 papers found, 24 cross-sectional studies with a total of 35,967 participants were included in this review. The general public lacked good knowledge of SARS and MERS at the early stage of epidemics. Some people's knowledge, attitude and practice (KAP) of COVID-19 had been improved, but the health behaviors of some special groups including children and their parents need to be strengthened. Negative emotions including fear and stigmatization occurred during the outbreaks. Reliable health information was needed to improve public awareness and mental health for infectious diseases. Health information from nonprofit, government and academic websites was more accurate than privately owned commercial websites and media websites. Conclusions: For educating and cultivating children, parents should obtain information from the official websites of authorities such as the World Health Organization (WHO) and national Centers for Disease Control, or from other sources endorsed by these authorities, rather than from a general search of the internet or social media.


[COVID-19 The challenges and opportunities for qualitative articles]/ COVID-19 Desafios e oportunidades para artigos qualitativos


title: Using the infection fatality rate to predict the evolution of Covid-19 in Brazil

text: In this work we are going to use estimates of Infection Fatality Rate (IFR) for Covid-19 in order to predict the evolution of Covid-19 in Brazil. To this aim, we are going to fit the parameters of the SIR model using the official deceased data available by governmental agencies. Furthermore, we are going to analyse the impact of social distancing policies on the transmission parameters


title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study

text: ABSTRACT OBJECTIVE To investigate the dynamics of viral RNA, IgM, and IgG and their relationships in patients with SARS-CoV-2 pneumonia over an 8-week period. DESIGN Retrospective, observational case series. SETTING Wenzhou Sixth Peoples Hospital PARTICIPANTS Thirty-three patients with laboratory confirmed SARS-CoV-2 pneumonia admitted to hospital. Data were collected from January 27 to April 10, 2020. MAIN OUTCOME MEASURES Throat swabs, sputum, stool, and blood samples were collected, and viral load was measured by reverse transcription PCR (RT-PCR). Specific IgM and IgG against spike protein (S), spike protein receptor binding domain (RBD), and nucleocapsid (N) were analyzed. RESULTS At the early stages of symptom onset, SARS-CoV-2 viral load is higher in throat swabs and sputum, but lower in stool. The median (IQR) time of undetectable viral RNA in throat swab, sputum, and stool was 18.5 (13.25-22) days, 22 (18.5-27.5) days, and 17 (11.5-32) days, respectively. In sputum, 17 patients (51.5%) had undetectable viral RNA within 22 days (short persistence), and 16 (48.5%) had persistent viral RNA more than 22 days (long persistence). Three patients (9.1%) had a detectable relapse of viral RNA in sputum within two weeks of their discharge from the hospital. One patient had persistent viral RNA for 59 days or longer. The median (IQR) seroconversion time of anti-S IgM, anti-RBD IgM, and anti-N IgM was 10.5 (7.75-15.5) days, 14 (9-24) days, and 10 (7-14) days, respectively. The median (IQR) seroconversion time of anti-S IgG, anti-RBD IgG, and anti-N IgG was 10 (7.25-16.5) days, 13 (9-17) days, and 10 (7-14) days, respectively. By week 8 after symptom onset, IgM were negative in many of the previously positive patients, and IgG levels remained less than 50% of the peak levels in more than 20% of the patients. In about 40% of the patients, anti-RBD IgG levels were 4-times higher in convalescence than in acute phase. SARS-CoV-2 RNA coexisted with antibodies for more than 50 days. Anti-RBD IgM and IgG levels, including anti-RBD IgM levels at presentation and peak time, were significantly higher in viral RNA short persistence patients than in long persistence patients. CONCLUSION This study adds important new information about the features of viral load and antibody dynamics of SARS-CoV-2. It is clear from these results that the viral RNA persists in sputum and stool specimens for a relatively long time in many patients. Anti-RBD may also serve as a potential protective antibody against SARS-CoV-2 infection, as viral persistence appears to be related to anti-RBD levels. Earlier treatment intervention also appears to be a factor in viral persistence.


title: SARS-CoV2 infection in farmed mink, Netherlands, April 2020

text: In April 2020, respiratory disease and increased mortality were observed in farmed mink on two farms in the Netherlands. In both farms, at least one worker had been found positive for SARS-CoV-2. Necropsies of the mink revealed interstitial pneumonia, and organ and swab samples tested positive for SARS-CoV-2 RNA by qPCR. Variations in viral genomes point at between-mink transmission on the farms and lack of infection link between the farms. Inhalable dust in the mink houses contained viral RNA, indicating possible exposure of workers.


title: Radiation Therapy Care During a Major Outbreak of COVID-19 in Wuhan

text: PURPOSE: The epidemic of coronavirus disease 2019 (COVID-19) challenges the prevention and protection of the cancer patients and the staff in the department of radiation oncology. METHODS: At the Hubei Cancer Hospital, we organized an emergency infection control team to lead special efforts to combat COVID-19 during this challenging time. RESULTS: Radiation therapy treatments were resumed on January 30th and have never stopped again at the hospital regardless of the circumstances of the ongoing outbreak. Between January 30th and the time of the writing, we have treated over 100 radiation therapy patients, with no incidence of on-site COVID-19 transmission between patients and health care workers in the duration. CONCLUSIONS: Our experience will help guide the practice in other regions that are or might be facing outbreaks of this disease.


title: COVID-19 incidence trends between April and June 2020: A global analysis

text: The study sought to investigate how the number of confirmed cases of COVID-19 have evolved in the most recent three months across the world, and what insights the trends may provide about the second half of the pandemic's first year using a situation analysis approach based on national income, temperature, trade intensity with China, and location defined by longitude and latitude. The study confirmed the negative relationship between COVID-19 cases and temperature. It contributed to the resolution of the conflicting results about latitude after organizing it into a categorical variable instead of its continuous form. This approach works because the average temperature in the 15 degrees S to 15 degrees N region remains similar to the average temperatures in both the Above 15 degrees N region and the Below 15 degrees S region during their summer months because the 15 degrees S to 15 degrees N region does not experience the marked seasonal changes in temperature. Given the negative association between temperature and case numbers, this suggests that countries in the 15 degrees S to 15 degrees N region might continue exhibiting the low numbers they have thus far exhibited through the second half of this year, even as numbers climb in the Below 15 degrees S region. To succeed, their policymakers must control importation of the disease by implementing effective testing, quarantining, and contact tracing for people entering their borders. Policymakers in countries Below 15 degrees S region may manage their inherent risks by applying lessons learned from countries in the Above 15 degrees N region during these past months. Such preventative measures may allow the world to avoid the drastic lockdown policies and facilitate rapid global economic recovery from this pandemic.


title: Public policy and economic dynamics of COVID-19 spread: a mathematical modeling study

text: Summary Background: With the COVID-19 pandemic infecting millions of people, largescale quarantine policies have been enacted across the globe. Understanding how to maximize the effectiveness of these policies while mitigating economic damage is essential. We develop a mathematical model with different levels of population health and economic risk to assess the impact of quarantine measures on deaths, hospitalizations, and economic output. Methods: We combine an extended SEIR model that has multiple levels of health risk and economic vulnerability with disease parameters for the COVID19 pandemic to study the effects of quarantine policies. We examine the dynamics of infectious disease transmission and its economic impact for one year. We populate our model with a baseline of 95.6 % of high-risk people and 85.6 % of low-risk people in quarantine. We use our model to simulate leaving the current quarantine restrictions in place indefinitely. We then assess a policy where quarantine restrictions for lower-risk groups are gradually relaxed. Finally, we simulate relaxing quarantine restrictions more quickly. To compare outbreak outcomes under the same quarantine policies using different disease parameters, we also perform a sensitivity analysis on the contagiousness of infected people, the strictness of social isolation measures, and the amount that public policymakers value the economy in setting quarantine restrictions. Findings: We first consider a baseline scenario with constant quarantine level, finding that in a population of 330,000,000 million, there are 32,023 deaths among those under 60 and 174,682 deaths among those over 60, there is a peak of 189,136 hospitalizations, and the economy relative to the beginning of the quarantine state is 1.4 % smaller. In the scenario where higher-risk people are strictly quarantined, and for others the quarantine is slowly relaxed, there are 63,776 deaths among those under 60, 85,880 deaths among those over 60, a peak of 341,321 hospitalizations, and the economy relative to the beginning of the quarantine state is 6% larger. In the scenario where quarantine is more quickly lifted, there are 25,720 deaths among those under 60, 214,718 deaths among those over 60, a peak of 341,321 hospitalizations, and economic output relative to the beginning of the quarantine state is 4.5 % smaller. Interpretation: Strict restrictions on high-risk patients and a gradual lifting of quarantine for low-risk patients results in a limited number of deaths and lesser economic damage. We recommend this kind of strategy, combined with policies lowering the contagiousness of the disease and making quarantine more tolerable and economically viable for individuals.


title: Re-analysis of SARS-CoV-2 infected host cell proteomics time-course data by impact pathway analysis and network analysis. A potential link with inflammatory response

text: The disease known as coronavirus disease 19 (COVID-19), potentially caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has hit the world hard, and has led to an unprecedent health and economic crisis. In order to develop treatment options able to stop or ameliorate SARS-CoV-2 effects, we need to understand the biology of the virus inside cells, but this kind of studies are still scarce. A recent study investigated translatome and proteome host cell changes induced in vitro by SARS-CoV-2. In the present study, we use the publicly available proteomics data from this study to re-analyze the mechanisms altered by the virus infection by impact pathways analysis and network analysis. Proteins linked to inflammatory response, but also proteins related to chromosome segregation during mitosis, were found to be regulated. The up-regulation of the inflammatory-related proteins observed could be linked to the propagation of inflammatory reaction and lung injury that is observed in advanced stages of COVID-19 patients.


title: The use of facemasks by the general population to prevent transmission of Covid 19 infection: A systematic review.

text: Background The pandemic of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2), has become a serious worldwide public health emergency. This systematic review aims to summarize the available evidence regarding the role of face mask in community settings in slowing the spread of respiratory viruses such as SARS- CoV-2. Methods The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were used for this review. A literature search using PUBMED, Google Scholar, and Cochrane database were performed using Medical subject heading (MeSH) words from the year 2000-2020. The articles focused on the use of masks and N95 respirators in healthcare workers were excluded. Results A total of 305 records were identified, out of which 14 articles were included in the review based upon quality and eligibility criteria. All the articles mentioned about the role of face masks in preventing the spread of respiratory viruses like influenza, SARS, and SARS-CoV-2, in the community or experimental setting. Studies also suggested that early initiation of face mask usage was more effective. Masks were also reported to be more effective in viruses that transmit easily from asymptomatic individuals, as is now known in SARS-CoV-2. Conclusion Theoretical, experimental, and clinical evidence suggested that usage of face masks in a general population offered significant benefit in preventing the spread of respiratory viruses especially in the pandemic situation, but its utility is limited by inconsistent adherence to mask usage.


title: The effect of control strategies that reduce social mixing on outcomes of the COVID-19 epidemic in Wuhan, China

text: BACKGROUND: In December 2019, a novel strain of SARS-CoV-2 emerged in Wuhan, China. Since then, the city of Wuhan has taken unprecedented measures and efforts in response to the outbreak. METHODS: We quantified the effects of control measures on population contact patterns in Wuhan, China, to assess their effects on the progression of the outbreak. We included the latest estimates of epidemic parameters from a transmission model fitted to data on local and internationally exported cases from Wuhan in the age-structured epidemic framework. Further, we looked at the age-distribution of cases. Lastly, we simulated lifting of the control measures by allowing people to return to work in a phased-in way, and looked at the effects of returning to work at different stages of the underlying outbreak. FINDINGS: Changes in mixing patterns may have contributed to reducing the number of infections in mid-2020 by 92% (interquartile range: 66-97%). There are benefits to sustaining these measures until April in terms of reducing the height of the peak, overall epidemic size in mid-2020 and probability that a second peak may occur after return to work. However, the modelled effects of social distancing measures vary by the duration of infectiousness and the role school children play in the epidemic. INTERPRETATION: Restrictions on activities in Wuhan, if maintained until April, would likely contribute to the reduction and delay the epidemic size and peak, respectively. However, there are some limitations to the analysis, including large uncertainties around estimates of R0 and the duration of infectiousness.


title: The clinical spectrum of encephalitis in COVID-19 disease: the ENCOVID multicentre study

text: Background: Several preclinical and clinical investigations have argued for nervous system involvement in SARS-CoV-2 infection. Some sparse case reports have described various forms of encephalitis in COVID-19 disease, but very few data have focused on clinical presentations, clinical course, response to treatment and outcomes yet. Objective: to describe the clinical phenotype, laboratory and neuroimaging findings of encephalitis associated with SARS-CoV-2 infection, their relationship with respiratory function and inflammatory parameters and their clinical course and response to treatment. Design: The ENCOVID multicentre study was carried out in 13 centres in northern Italy between February 20th and May 31st, 2020. Only patients with altered mental status and at least two supportive criteria for encephalitis with full infectious screening, CSF, EEG, MRI data and a confirmed diagnosis of SARS-CoV-2 infection were included. Clinical presentation and laboratory markers, severity of COVID-19 disease, response to treatment and outcomes were recorded. Results: Out of 45 cases screened, twenty-five cases of encephalitis positive for SARS-CoV-2 infection with full available data were included. The most common symptoms at onset were delirium (68%), aphasia/dysarthria (24%) and seizures (24%). CSF showed hyperproteinorrachia and/or pleocytosis in 68% of cases whereas SARS-CoV-2 RNA by RT-PCR resulted negative. Based on MRI, cases were classified as ADEM (n=3), limbic encephalitis (LE, n=2), encephalitis with normal imaging (n=13) and encephalitis with MRI alterations (n=7). ADEM and LE cases showed a delayed onset compared to the other encephalitis (p=0.001) and were associated with previous more severe COVID-19 respiratory involvement. Patients with MRI alterations exhibited worse response to treatment and final outcomes compared to other encephalitis. Conclusions and relevance: We found a wide clinical spectrum of encephalitis associated with COVID19 infection, underlying different pathophysiological mechanisms. Response to treatment and final outcome strongly depended on specific CNS-manifestations.


title: Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics

text: We report the development of a new technology for simultaneous quantitative detection of multiple targets in a single sample. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. STAR demonstrated similar or better sensitivity and precision compared to two commonly used methods, SYBR Green-based and TaqMan probe-based real-time reverse transcriptase-polymerase chain reaction. STAR can be used as a flexible platform for building a variety of applications to monitor gene expression, from single gene assays to assays analyzing the expression level of multiple genes. Using severe acute respiratory syndrome (SARS) corona virus as a model system, STAR technology detected single copies of the viral genome in a two-gene multiplex. Blinded studies using RNA extracted from various tissues of a SARS-infected individual showed that STAR correctly identified all samples containing SARS virus and yielded negative results for non-SARS control samples. Using alternate priming strategies, STAR technology can be adapted to transcriptional profiling studies without requiring a priori sequence information. Thus, STAR technology offers a flexible platform for development of highly multiplexed assays in gene expression analysis and molecular diagnostics.


title: ‘All the single ladies’ as the ideal academic in times of Covid-19?

text: Much of what has hitherto been written about women?s lived experiences of the coronavirus pandemic takes their status as mothers and the spouses of men for granted Skewed care demands on women researchers working from home may translate into individual career disadvantage and cumulative, large-scale gender inequalities in the future, which is undeniably a serious issue However, the narrative that single, childfree women must currently, by contrast, be unconcernedly enjoying a surge of productivity needs to be nuanced Therefore, with this paper, I autoethnographically discuss how living alone in the context of the Covid-19 pandemic provides its own set of circumstances and is hardly problem-free, which affects how one can deal with issues of academic productivity and work-life balance Also, I take issue with the premise that our productivity is the golden standard against which we and our worth should be measured while we are living through a global crisis


title: Understand Research Hotspots Surrounding COVID-19 and Other Coronavirus Infections Using Topic Modeling

text: Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that causes severe respiratory illness in humans, which eventually results in the current outbreak of novel coronavirus disease (COVID-19) around the world. The research community is interested to know what are the hotspots in coronavirus (CoV) research and how much is known about COVID-19. This study aimed to evaluate the characteristics of publications involving coronaviruses as well as COVID-19 by using a topic modeling analysis. Methods: We extracted all abstracts and retained the most informative words from the COVID-19 Open Research Dataset, which contains all the 35,092 pieces of coronavirus related literature published up to March 20, 2020. Using Latent Dirichlet Allocation modeling, we trained an eight-topic model from the corpus. We then analyzed the semantic relationships between topics and compared the topic distribution between COVID-19 and other CoV infections. Results: Eight topics emerged overall: clinical characterization, pathogenesis research, therapeutics research, epidemiological study, virus transmission, vaccines research, virus diagnostics, and viral genomics. It was observed that COVID-19 research puts more emphasis on clinical characterization, epidemiological study, and virus transmission at present. In contrast, topics about diagnostics, therapeutics, vaccines, genomics and pathogenesis only accounted for less than 10% or even 4% of all the COVID-19 publications, much lower than those of other CoV infections. Conclusions: These results identified knowledge gaps in the area of COVID-19 and offered directions for future research. Keywords: COVID-19, coronavirus, topic modeling, hotspots, text mining


title: COVID-19 in Latin America: Contrasting phylodynamic inference with epidemiological surveillance.

text: Introduction: SARS-CoV-2 infection has represented the one of the largest challenges for humanity. This virus was first detected in Latin America and the Caribbean (LAC) in Brazil in February 26, 2020 and it has revealed important gaps in infectious disease surveillance that must be covered. Phylodynamic analysis is a tool that can help to monitor and adapt traditional surveillance measures in order to cover those. Therefore, this work aims to contrast data driven from epidemiologic surveillance in LAC with parameters inferred from phylodynamic analysis of reported genomes of SARS-CoV-2 across different LAC countries Methods: We obtained epidemiological data from daily reports provided by European Centre for Disease Prevention and Control up to 13th May, 2020. We estimated Effective Reproductive Number (Re) and calculated epidemic curves with exponential growth (EG) and maximum likelihood (ML) methods. SARS-CoV-2 phylodynamic in Latin-American was analyzed using sequences reported in GISAID for Central and South America up to May 13th 2020. Sequences were aligned, and ML phylogeny was constructed. Coalescent model Birth Death SIR (serial) was run, and SIR trajectories from the birth-death SIR model were plotted. Results: A total of 404,448 cases were reported up to 13th May 2020. Overall reproduction number for Latin America, estimated through the EG and ML methods, were 1.424 (IC95% 1.422 to 1.426) and 1.305 (IC95% 1.299 to 1.311) respectively. Phylodynamic analysis for Latin America showed an overall Re of 1.27 (IC95% 1.07 to 1.49). We did not find statistically significant differences between epidemiological and phylodynamic data at the cut-off time, except for Brazil. Discussion: Our results support that epidemiological and genomic surveillance are two complementary approaches. Evidence suggests that even with a low number of sequences proper estimations of Re could be performed. We suggest that countries, especially developing countries, should consider to add genomic surveillance to their systems for monitoring and adapting epidemiological surveillance of SARS-CoV-2.


title: Emerging and re-emerging human infectious diseases: A systematic review of the role of wild animals with a focus on public health impact

text: Infectious diseases continue to impose unpredictable burdens on global health and economies, a subject that requires constant research and updates. In this sense, the objective of the present article was to review studies on the role of wild animals as reservoirs and/or dispersers of etiological agents of human infectious diseases in order to compile data on the main wild animals and etiological agents involved in zoonotic outbreaks. A systematic review was carried out using PRISMA guidelines, using the PubMed, Scopus and SciELO platforms as data banks. The descriptors used were 'zoonosis', 'human infectious diseases' and 'wild animals'. The results show that wild animals (mainly bats, birds and primates) play an important role in the dissemination of etiological agents (mainly viruses, as a new coronavirus called 2019 Novel Coronavirus) in extensive geographic regions. Moreover, these wild animal organisms can act as the site for essential biotic synergy among several pathogenic microorganisms, promoting a higher rate of adaptation, mutation and even genetic recombination, with consequent stimulation of new strains and subtypes, inducing new infectious agents with unknown virulent potential. In conclusion, the monitoring of these diseases and adequate preparation for possible epidemics and pandemics are fundamental conditions for the mitigation of their future impact. The zoonotic threat of these etiological agents and the impact on public health can be enormous as shown by the ongoing epidemic of 2019 novel coronavirus (2019- nCoV) infections.


title: How lethal is the novel coronavirus, and how many undetected cases there are? The importance of being tested.

text: There is big concern for estimating the lethality and the extent of undetected infections associated with the novel coronavirus SARS-CoV2 outbreak. While detailed epidemiological models are certainly needed, I suggest here an orthogonal approach based on a minimum number of parameters robustly fitted from the cumulative data easily accessible for all countries at the John Hopkins University database that became the worldwide reference for the pandemics. I show that, after few days from the beginning of the outbreak, the apparent death rate can be extrapolated to infinite time through regularized regression such as rescaled ridge regression. The variation from country to country of these extrapolated death rates appears to depend almost only (r^2=0.91) on the ratio between performed tests and detected cases even when the instantaneous apparent lethality rates are as different as 9% in Italy and 0.4% in Germany. Extrapolating to the limit of infinite number of tests, I obtain a death rate of 0.012+/- 0.012, in agreement with other estimates. The inverse relationship between the extrapolated death rate and the intensity tests allows estimating that more than 50% of cases were undetected in most countries, with more than 90% undetected cases in countries severely hit by the epidemics such as Italy. Finally, I propose to adopt the ratio between the cumulative number of recovered and deceased persons as an indicator that can anticipate the halting of the epidemics.


title: Emerging phylogenetic structure of the SARS-CoV-2 pandemic

text: Since spilling over into humans, SARS-CoV-2 has rapidly spread across the globe, accumulating significant genetic diversity. The structure of this genetic diversity, and whether it reveals epidemiological insights, are fundamental questions for understanding the evolutionary trajectory of this virus. Here we use a recently developed phylodynamic approach to uncover phylogenetic structures underlying the SARS-CoV-2 pandemic. We find support for three SARS-CoV-2 lineages co-circulating, each with significantly different demographic dynamics concordant with known epidemiological factors. For example, Lineage C emerged in Europe with a high growth rate in late February, just prior to the exponential increase in cases in several European countries. Mutations that characterize Lineage C in particular are non-synonymous and occur in functionally important gene regions responsible for viral replication and cell entry. Even though Lineages A and B had distinct demographic patterns, they were much more difficult to distinguish. Continuous application of phylogenetic approaches to track the evolutionary epidemiology of SARS-CoV-2 lineages will be increasingly important to validate the efficacy of control efforts and monitor significant evolutionary events in the future.