scholarly journals An Unsupervised Algorithm for Host Identification in Flaviviruses

Life ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 442
Author(s):  
Phuoc Truong Nguyen ◽  
Santiago Garcia-Vallvé ◽  
Pere Puigbò
Keyword(s):  
Codon Usage ◽  
Emerging Viruses ◽  
Virus Group ◽  
Host Type ◽  
Zoonotic Viruses ◽  
Selective Forces ◽  
Novel Method ◽  
Host Identification ◽  
And Control

Early characterization of emerging viruses is essential to control their spread, such as the Zika Virus outbreak in 2014. Among other non-viral factors, host information is essential for the surveillance and control of virus spread. Flaviviruses (genus Flavivirus), akin to other viruses, are modulated by high mutation rates and selective forces to adapt their codon usage to that of their hosts. However, a major challenge is the identification of potential hosts for novel viruses. Usually, potential hosts of emerging zoonotic viruses are identified after several confirmed cases. This is inefficient for deterring future outbreaks. In this paper, we introduce an algorithm to identify the host range of a virus from its raw genome sequences. The proposed strategy relies on comparing codon usage frequencies across viruses and hosts, by means of a normalized Codon Adaptation Index (CAI). We have tested our algorithm on 94 flaviviruses and 16 potential hosts. This novel method is able to distinguish between arthropod and vertebrate hosts for several flaviviruses with high values of accuracy (virus group 91.9% and host type 86.1%) and specificity (virus group 94.9% and host type 79.6%), in comparison to empirical observations. Overall, this algorithm may be useful as a complementary tool to current phylogenetic methods in monitoring current and future viral outbreaks by understanding host–virus relationships.

scholarly journals Bat viruses and diseases

2009 ◽  
Vol 30 (4) ◽  
pp. 122
Author(s):  
Lin-Fa Wang
Keyword(s):  
Disease Outbreaks ◽  
Vital Role ◽  
Clinical Consequence ◽  
Emerging Viruses ◽  
Mammal Species ◽  
Livestock Disease ◽  
Geographically Dispersed ◽  
Zoonotic Viruses ◽  
And Control ◽  
Reservoir Hosts

Bats, representing approximately 20% of mammal species, are the most abundant, diverse and geographically dispersed vertebrates on earth. Bats of various species have recently been identified as the reservoir hosts of many emerging viruses responsible for severe human and livestock disease outbreaks. These include Hendra and Nipah viruses, SARS coronavirus, Ebola viruses, Melaka virus and others. Australian scientists played a vital role in the discovery and/or characterisation of many of these emerging bat viruses. While these viruses result in significant morbidity and mortality in other mammals, they appear to cause no clinical consequence in bats under natural or experimental infection. Understanding this key difference in pathogenesis and the mechanism of virus spillover from bats to other mammals will be critical for our effort to prevent and control future disease outbreaks caused by bat-borne zoonotic viruses.

Introduction

2018 ◽  
Author(s):  
Elizabeth S. Radcliffe
Keyword(s):  
Early Modern ◽  
Historical Background ◽  
Consistent Picture ◽  
And Control ◽  
Good And Evil

The Introduction offers, first, a brief historical background to Hume’s theory of the passions, which is further elaborated in the APPENDIX. Foremost among the theses of the early modern rationalists—like Reynolds, Senault, Descartes, Cudworth, and Clarke—to which Hume is responding are: that many passions left unregulated lead to the pursuit of unsuitable objects, that reason can overcome the pernicious influence of the passions and control our actions, and that the passions are states that represent good and evil. Second, the Introduction presents a sketch of Hume’s characterization of reason and passion and his account of their relationship. Third, it explains the method of interpretation used in this book and previews its chapters. The approach is coherentist: to present an intelligible and consistent picture of Hume’s theory of passion and action, accounting for as many of the relevant texts as possible.

scholarly journals Design, Construction, and Control for an Underwater Vehicle Type Sepiida

Robotica ◽  
2020 ◽  
pp. 1-18
Author(s):  
M. Garcia ◽  
P. Castillo ◽  
E. Campos ◽  
R. Lozano
Keyword(s):  
Embedded System ◽  
Closed Loop ◽  
Underwater Vehicle ◽  
Mathematical Representation ◽  
Closed Loop System ◽  
Vehicle Type ◽  
Mathematical Equations ◽  
And Control ◽  
Design Construction

SUMMARY A novel underwater vehicle configuration with an operating principle as the Sepiida animal is presented and developed in this paper. The mathematical equations describing the movements of the vehicle are obtained using the Newton–Euler approach. An analysis of the dynamic model is done for control purposes. A prototype and its embedded system are developed for validating analytically and experimentally the proposed mathematical representation. A real-time characterization of one mass is done to relate the pitch angle with the radio of displacement of the mass. In addition, first validation of the closed-loop system is done using a linear controller.

scholarly journals Clinical characterization of dysautonomia in long COVID-19 patients

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicolas Barizien ◽  
Morgan Le Guen ◽  
Stéphanie Russel ◽  
Pauline Touche ◽  
Florent Huang ◽  
...  
Keyword(s):  
Mixed Models ◽  
Repeated Measures ◽  
Physical Medicine ◽  
Persistent Symptoms ◽  
Index Changes ◽  
Changes Over Time ◽  
And Control ◽  
Testing Group ◽  
Over Time

AbstractIncreasing numbers of COVID-19 patients, continue to experience symptoms months after recovering from mild cases of COVID-19. Amongst these symptoms, several are related to neurological manifestations, including fatigue, anosmia, hypogeusia, headaches and hypoxia. However, the involvement of the autonomic nervous system, expressed by a dysautonomia, which can aggregate all these neurological symptoms has not been prominently reported. Here, we hypothesize that dysautonomia, could occur in secondary COVID-19 infection, also referred to as “long COVID” infection. 39 participants were included from December 2020 to January 2021 for assessment by the Department of physical medicine to enhance their physical capabilities: 12 participants with COVID-19 diagnosis and fatigue, 15 participants with COVID-19 diagnosis without fatigue and 12 control participants without COVID-19 diagnosis and without fatigue. Heart rate variability (HRV) during a change in position is commonly measured to diagnose autonomic dysregulation. In this cohort, to reflect HRV, parasympathetic/sympathetic balance was estimated using the NOL index, a multiparameter artificial intelligence-driven index calculated from extracted physiological signals by the PMD-200 pain monitoring system. Repeated-measures mixed-models testing group effect were performed to analyze NOL index changes over time between groups. A significant NOL index dissociation over time between long COVID-19 participants with fatigue and control participants was observed (p = 0.046). A trend towards significant NOL index dissociation over time was observed between long COVID-19 participants without fatigue and control participants (p = 0.109). No difference over time was observed between the two groups of long COVID-19 participants (p = 0.904). Long COVID-19 participants with fatigue may exhibit a dysautonomia characterized by dysregulation of the HRV, that is reflected by the NOL index measurements, compared to control participants. Dysautonomia may explain the persistent symptoms observed in long COVID-19 patients, such as fatigue and hypoxia. Trial registration: The study was approved by the Foch IRB: IRB00012437 (Approval Number: 20-12-02) on December 16, 2020.

scholarly journals The Combined Effect of Weaning Stress and Immune Activation during Pig Gestation on Serum Cytokine and Analyte Concentrations

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2274
Author(s):  
Haley E. Rymut ◽  
Laurie A. Rund ◽  
Courtni R. Bolt ◽  
Maria B. Villamil ◽  
Bruce R. Southey ◽  
...  
Keyword(s):  
Immune Activation ◽  
Management Practices ◽  
Interleukin 1 ◽  
Interleukin 2 ◽  
Blood Chemistry ◽  
Respiratory Syndrome Virus ◽  
Weaning Stress ◽  
And Control ◽  
Metabolic Hormone

Weaning stress can elicit changes in the metabolic, hormone and immune systems of pigs and interact with prolonged disruptions stemming from maternal immune activation (MIA) during gestation. The present study advances the characterization of the combined effects of weaning stress and MIA on blood chemistry, immune and hormone indicators that inform on the health of pigs. Three-week-old female and male offspring of control gilts or gilts infected with the porcine reproductive and respiratory syndrome virus were allocated to weaned or nursed groups. The anion gap and bilirubin profiles suggest that MIA enhances tolerance to the effects of weaning stress. Interleukin 1 beta and interleukin 2 were highest among weaned MIA females, and cortisol was higher among weaned relative to nursed pigs across sexes. Canonical discriminant analysis demonstrated that weaned and nursed pigs have distinct chemistry profiles, whereas MIA and control pigs have distinct cytokine profiles. The results from this study can guide management practices that recognize the effects of the interaction between MIA and weaning stress on the performance and health of pigs.

scholarly journals Genotypic Characterization of Antimicrobial Resistant Salmonella spp. Strains from Three Poultry Processing Plants in Colombia

Foods ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 491
Author(s):  
Alejandra Ramirez-Hernandez ◽  
Ana K. Carrascal-Camacho ◽  
Andrea Varón-García ◽  
Mindy M. Brashears ◽  
Marcos X. Sanchez-Plata
Keyword(s):  
Antimicrobial Resistance ◽  
Salmonella Spp ◽  
Microbial Profile ◽  
Antimicrobial Resistance Genes ◽  
Processing Plants ◽  
Poultry Processing ◽  
Paratyphi B ◽  
And Control ◽  
Sequence Types

The poultry industry in Colombia has implemented several changes and measures in chicken processing to improve sanitary operations and control pathogens’ prevalence. However, there is no official in-plant microbial profile reference data currently available throughout the processing value chains. Hence, this research aimed to study the microbial profiles and the antimicrobial resistance of Salmonella isolates in three plants. In total, 300 samples were collected in seven processing sites. Prevalence of Salmonella spp. and levels of Enterobacteriaceae were assessed. Additionally, whole-genome sequencing was conducted to characterize the isolated strains genotypically. Overall, the prevalence of Salmonella spp. in each establishment was 77%, 58% and 80% for plant A, B, and C. The mean levels of Enterobacteriaceae in the chicken rinsates were 5.03, 5.74, and 6.41 log CFU/mL for plant A, B, and C. Significant reductions were identified in the counts of post-chilling rinsate samples; however, increased levels were found in chicken parts. There were six distinct Salmonella spp. clusters with the predominant sequence types ST32 and ST28. The serotypes Infantis (54%) and Paratyphi B (25%) were the most commonly identified within the processing plants with a high abundance of antimicrobial resistance genes.

scholarly journals 491. Aerosol-Generating Medical Procedures: Transmission of SARS-CoV-2 and Emerging Viruses

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S312-S312
Author(s):  
Seth D Judson ◽  
Vincent J Munster
Keyword(s):  
High Risk ◽  
Severe Disease ◽  
Experimental Studies ◽  
Virus Transmission ◽  
Nosocomial Transmission ◽  
Medical Procedures ◽  
Emerging Viruses ◽  
Zoonotic Viruses ◽  
Increased Risk ◽  
Hospital Acquired

Abstract Background During the pandemic of coronavirus disease 2019 (COVID-19), many questions arose regarding risks for hospital-acquired or nosocomial transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Aerosol generating medical procedures (AGMPs), techniques that can generate infectious, virus-laden aerosols, could potentially amplify transmission among healthcare workers (HCWs). Thus, it was widely recommended that HCWs use airborne precautions when performing AGMPs. However, in clinical settings it is often unclear what procedures constitute AGMPs and how the risk varies by procedure or pathogen. We set out to further define AGMPs and assess the risk for nosocomial transmission of SARS-CoV-2 and other high-risk viruses via AGMPs. Methods We identified potential AGMPs and emerging viruses that were high-risk for nosocomial transmission through reviewing experimental and clinical data. Potential AGMPs were those associated with previous virus transmission or mechanically capable of transmission. High-risk viruses were defined as those that cause severe disease in humans for which limited therapies or interventions exist, are infectious via aerosols in humans or non-human primates (NHPs), found in the respiratory tract of infected humans or NHPs, and had previous evidence of nosocomial transmission. Results We identified multiple potential AGMPs, which could be divided into those that generate aerosols or induce a patient to form aerosols, as well as eight families of high-risk viruses. All of the viruses were emerging zoonotic RNA viruses. In the family Coronaviridae, we identified potential evidence for SARS-CoV-1, MERS-CoV, and SARS-CoV-2 transmission via AGMPs. SARS-CoV-1 and SARS-CoV-2 were also found to be similarly stable when aerosolized. Conclusion Multiple emerging zoonotic viruses pose a high risk for nosocomial transmission through a variety of AGMPs. Given the similar stability of SARS-CoV-2 with SARS-CoV-1 when aerosolized and prior nosocomial transmission of SARS-CoV-1 via AGMPs, we suspect that certain AGMPs pose an increased risk for SARS-CoV-2 transmission. Additional experimental studies and on-site clinical sampling during AGMPs are necessary to further risk stratify AGMPs. Disclosures All Authors: No reported disclosures

scholarly journals Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Giovanni Franzo ◽  
Claudia Maria Tucciarone ◽  
Matteo Legnardi ◽  
Mattia Cecchinato
Keyword(s):  
Codon Usage ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Accessory Proteins ◽  
Effective Number ◽  
Genome Composition ◽  
Infectious Bronchitis ◽  
Selective Forces ◽  
Effective Number Of Codons

Abstract Background Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. Results The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. Conclusions The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity.

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