scholarly journals The Unique Phylogenetic Position of a Novel Tick-Borne Phlebovirus Ensures an Ixodid Origin of the GenusPhlebovirus

mSphere ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Keita Matsuno ◽  
Masahiro Kajihara ◽  
Ryo Nakao ◽  
Naganori Nao ◽  
Akina Mori-Kajihara ◽  
...  
Keyword(s):  
Public Health ◽  
Infectious Diseases ◽  
Rna Viruses ◽  
Recent Common Ancestor ◽  
Severe Illness ◽  
Ixodes Persulcatus ◽  
Hard Tick ◽  
Ancestral State ◽  
Content Type ◽  
Severe Fever

ABSTRACTThe recent emergence of novel tick-borne RNA viruses has complicated the epidemiological landscape of tick-borne infectious diseases, posing a significant challenge to public health systems that seek to counteract tick-borne diseases. The identification of two novel tick-borne phleboviruses (TBPVs), severe fever with thrombocytopenia syndrome virus (SFTSV) and Heartland virus (HRTV), as causative agents of severe illness in humans has accelerated the investigation and discoveries of novel TBPVs. In the present study, we isolated a novel TBPV designated Mukawa virus (MKWV) from host-questingIxodes persulcatusfemales captured in Japan. Genetic characterization revealed that MKWV is a member of the genusPhlebovirusin the familyPhenuiviridae. Interestingly, MKWV is genetically distinct from other known TBPVs and shares a most recent common ancestor with mosquito/sandfly-borne (insect-borne) phleboviruses. Despite its genetic similarity to insect-borne phleboviruses, the molecular footprints of its viral proteins and its biological characteristics define MKWV as a tick-borne virus that can be transmitted to mammals. A phylogenetic ancestral-state reconstruction for arthropod vectors of phleboviruses including MKWV based on viral L segment sequences indicated that ticks likely harbored ancestral phleboviruses that evolved into both the tick-borne and MKWV/insect-borne phlebovirus lineages. Overall, our findings suggest that most of the phlebovirus evolution has occurred in hard ticks to generate divergent viruses, which may provide a seminal foundation for understanding the mechanisms underlying the evolution and emergence of pathogenic phleboviruses, such as Rift Valley fever virus and SFTSV/HRTV.IMPORTANCEThe emergence of novel tick-borne RNA viruses causing severe illness in humans has complicated the epidemiological landscape of tick-borne diseases, requiring further investigation to safeguard public health. In the present study, we discovered a novel tick-borne phlebovirus fromIxodes persulcatusticks in Japan. While its viral RNA genome sequences were similar to those of mosquito/sandfly-borne viruses, molecular and biological footprints confirmed that this is a tick-borne virus. The unique evolutionary position of the virus allowed us to estimate the ancestral phlebovirus vector, which was likely a hard tick. Our findings may provide a better understanding of the evolution and emergence of phleboviruses associated with emerging infectious diseases, such as severe fever with thrombocytopenia syndrome (SFTS) and Heartland virus disease.

scholarly journals Genomic epidemiology of tuberculosis in eastern Malaysia: insights for strengthening public health responses

2021 ◽  
Vol 7 (5) ◽  
Author(s):  
Arnold Bainomugisa ◽  
Ella M. Meumann ◽  
Giri Shan Rajahram ◽  
Rick Twee-Hee Ong ◽  
Lachlan Coin ◽  
...  
Keyword(s):  
Public Health ◽  
Type Species ◽  
Multidrug Resistant ◽  
Resistant Isolate ◽  
Recent Common Ancestor ◽  
Resistance Mutations ◽  
Content Type ◽  
Genomic Epidemiology ◽  
Link Type ◽  
Lineage 2

Tuberculosis is a leading public health priority in eastern Malaysia. Knowledge of the genomic epidemiology of tuberculosis can help tailor public health interventions. Our aims were to determine tuberculosis genomic epidemiology and characterize resistance mutations in the ethnically diverse city of Kota Kinabalu, Sabah, located at the nexus of Malaysia, Indonesia, Philippines and Brunei. We used an archive of prospectively collected Mycobacterium tuberculosis samples paired with epidemiological data. We collected sputum and demographic data from consecutive consenting outpatients with pulmonary tuberculosis at the largest tuberculosis clinic from 2012 to 2014, and selected samples from tuberculosis inpatients from the tertiary referral centre during 2012–2014 and 2016–2017. Two hundred and eight M . tuberculosis sequences were available for analysis, representing 8 % of cases notified during the study periods. Whole-genome phylogenetic analysis demonstrated that most strains were lineage 1 (195/208, 93.8 %), with the remainder being lineages 2 (8/208, 3.8 %) or 4 (5/208, 2.4 %). Lineages or sub-lineages were not associated with patient ethnicity. The lineage 1 strains were diverse, with sub-lineage 1.2.1 being dominant (192, 98 %). Lineage 1.2.1.3 isolates were geographically most widely distributed. The greatest diversity occurred in a border town sub-district. The time to the most recent common ancestor for the three major lineage 1.2.1 clades was estimated to be the year 1966 (95 % HPD 1948–1976). An association was found between failure of culture conversion by week 8 of treatment and infection with lineage 2 (4/6, 67 %) compared with lineage 1 strains (4/83, 5 %) (P<0.001), supporting evidence of greater virulence of lineage 2 strains. Eleven potential transmission clusters (SNP difference ≤12) were identified; at least five included people living in different sub-districts. Some linked cases spanned the whole 4-year study period. One cluster involved a multidrug-resistant tuberculosis strain matching a drug-susceptible strain from 3 years earlier. Drug resistance mutations were uncommon, but revealed one phenotype–genotype mismatch in a genotypically multidrug-resistant isolate, and rare nonsense mutations within the katG gene in two isolates. Consistent with the regionally mobile population, M. tuberculosis strains in Kota Kinabalu were diverse, although several lineage 1 strains dominated and were locally well established. Transmission clusters – uncommonly identified, likely attributable to incomplete sampling – showed clustering occurring across the community, not confined to households or sub-districts. The findings indicate that public health priorities should include active case finding and early institution of tuberculosis management in mobile populations, while there is a need to upscale effective contact investigation beyond households to include other contacts within social networks.

scholarly journals Tissue Tropism and Transmission Ecology Predict Virulence of Human RNA Viruses

2019 ◽  
Author(s):  
Liam Brierley ◽  
Amy B. Pedersen ◽  
Mark E. J. Woolhouse
Keyword(s):  
Public Health ◽  
Machine Learning ◽  
Risk Factors ◽  
Random Forest ◽  
Infectious Diseases ◽  
Rna Viruses ◽  
Rna Virus ◽  
Tissue Tropism ◽  
Virus Species ◽  
Ecological Traits

AbstractNovel infectious diseases continue to emerge within human populations. Predictive studies have begun to identify pathogen traits associated with emergence. However, emerging pathogens vary widely in virulence, a key determinant of their ultimate risk to public health. Here, we use structured literature searches to review the virulence of each of the 214 known human-infective RNA virus species. We then use a machine learning framework to determine whether viral virulence can be predicted by ecological traits including human-to-human transmissibility, transmission routes, tissue tropisms and host range. Using severity of clinical disease as a measurement of virulence, we identified potential risk factors using predictive classification tree and random forest ensemble models. The random forest model predicted literature-assigned disease severity of test data with 90.3% accuracy, compared to a null accuracy of 74.2%. In addition to viral taxonomy, the ability to cause systemic infection, having renal and/or neural tropism, direct contact or respiratory transmission, and limited (0 < R0 ≤ 1) human-to-human transmissibility were the strongest predictors of severe disease. We present a novel, comparative perspective on the virulence of all currently known human RNA virus species. The risk factors identified may provide novel perspectives in understanding the evolution of virulence and elucidating molecular virulence mechanisms. These risk factors could also improve planning and preparedness in public health strategies as part of a predictive framework for novel human infections.Author SummaryNewly emerging infectious diseases present potentially serious threats to global health. Although studies have begun to identify pathogen traits associated with the emergence of new human diseases, these do not address why emerging infections vary in the severity of disease they cause, often termed ‘virulence’. We test whether ecological traits of human viruses can act as predictors of virulence, as suggested by theoretical studies. We conduct the first systematic review of virulence across all currently known human RNA virus species. We adopt a machine learning approach by constructing a random forest, a model that aims to optimally predict an outcome using a specific structure of predictors. Predictions matched literature-assigned ratings for 28 of 31 test set viruses. Our predictive model suggests that higher virulence is associated with infection of multiple organ systems, nervous systems or the renal systems. Higher virulence was also associated with contact-based or airborne transmission, and limited capability to transmit between humans. These risk factors may provide novel starting points for questioning why virulence should evolve and identifying causative mechanisms of virulence. In addition, our work could suggest priority targets for infectious disease surveillance and future public health risk strategies.BlurbComparative analysis using machine learning shows specificity of tissue tropism and transmission biology can act as predictive risk factors for virulence of human RNA viruses.

The dangers of infection: school medical inspection in Brazil (the 1910s)

2017 ◽  
Vol 46 (2) ◽  
pp. 150-163 ◽  
Author(s):  
Heloísa Helena Pimenta Rocha ◽  
Henrique Mendonça da Silva
Keyword(s):  
Public Health ◽  
Nineteenth Century ◽  
Infectious Diseases ◽  
Design Methodology ◽  
Historical Analysis ◽  
Late Nineteenth Century ◽  
International Debate ◽  
Content Type ◽  
Social Hygiene ◽  
Late Nineteenth

Purpose The purpose of this paper is to investigate the introduction of school medical inspection (SMI) in Rio de Janeiro and São Paulo (Brazil) during the 1910s, in a process aligned with the international debate that, since the late nineteenth century, sustained the need of services that focused on the sanitary inspection of schools and their students. It analyzes the purposes guiding the creation of these services and their connections to the spheres of public health and education, highlighting the role taken by the concerns about issues such as the control of infectious diseases, particularly tuberculosis. Design/methodology/approach The study consists of a historical analysis using as sources the legislation and documents produced by the SMI. The documents are examined in correlation with the positions defended at international conferences held at the period. Findings The study evidences the intricacies of the introduction of SMI services in the Brazilian states that were pioneers in this area. It examines their relations to guidelines established in international forums, which certainly played an important role in the Brazilian efforts. It also allowed to highlight the relations between efforts to create medical inspections in school and those aiming at fighting infectious diseases. Originality/value The paper contributes to a better comprehension of the efforts regarding social hygiene and particularly the hygiene of schools and their students in a period in which the state takes greater responsibilities for its population.

scholarly journals Thermotoga lettingae Can Salvage Cobinamide To Synthesize Vitamin B12

2013 ◽  
Vol 79 (22) ◽  
pp. 7006-7012 ◽  
Author(s):  
Nicholas C. Butzin ◽  
Michael A. Secinaro ◽  
Kristen S. Swithers ◽  
J. Peter Gogarten ◽  
Kenneth M. Noll
Keyword(s):  
Gene Cluster ◽  
Common Ancestor ◽  
De Novo ◽  
Recent Common Ancestor ◽  
Vitamin B ◽  
Ancestral State ◽  
Salvage Pathway ◽  
Content Type ◽  
Most Recent Common Ancestor

ABSTRACTWe recently reported that theThermotogalesacquired the ability to synthesize vitamin B12by acquisition of genes from two distantly related lineages,ArchaeaandFirmicutes(K. S. Swithers et al., Genome Biol. Evol. 4:730–739, 2012). Ancestral state reconstruction suggested that the cobinamide salvage gene cluster was present in theThermotogales' most recent common ancestor. We also predicted thatThermotoga lettingaecould not synthesize B12de novobut could use the cobinamide salvage pathway to synthesize B12. In this study, these hypotheses were tested, and we found thatTt. lettingaedid not synthesize B12de novobut salvaged cobinamide. The growth rate ofTt. lettingaeincreased with the addition of B12or cobinamide to its medium. It synthesized B12when the medium was supplemented with cobinamide, and no B12was detected in cells grown on cobinamide-deficient medium. Upstream of the cobinamide salvage genes is a putative B12riboswitch. In other organisms, B12riboswitches allow for higher transcriptional activity in the absence of B12. WhenTt. lettingaewas grown with no B12, the salvage genes were upregulated compared to cells grown with B12or cobinamide. Another gene cluster with a putative B12riboswitch upstream is thebtuFCDABC transporter, and it showed a transcription pattern similar to that of the cobinamide salvage genes. The BtuF proteins from species that can and cannot salvage cobinamides were shownin vitroto bind both B12and cobinamide. These results suggest thatThermotogalesspecies can use the BtuFCD transporter to import both B12and cobinamide, even if they cannot salvage cobinamide.

scholarly journals Diversity, Distribution, and Evolution of Tomato Viruses in China Uncovered by Small RNA Sequencing

2017 ◽  
Vol 91 (11) ◽  
Author(s):  
Chenxi Xu ◽  
Xuepeng Sun ◽  
Angela Taylor ◽  
Chen Jiao ◽  
Yimin Xu ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Length Distribution ◽  
Recent Common Ancestor ◽  
Viral Diseases ◽  
Small Rna Sequencing ◽  
Evolutionary Analysis ◽  
Virus Species ◽  
Tomato Production ◽  
Content Type ◽  
A Genome

ABSTRACT Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here, we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified, including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with cold spots and hot spots. Most samples were coinfected by multiple viruses, and the majority of identified viruses are positive-sense single-stranded RNA viruses. Evolutionary analysis of one of the most dominant tomato viruses, Tomato yellow leaf curl virus (TYLCV), predicts its origin and the time back to its most recent common ancestor. The broadly sampled data have enabled us to identify several unreported viruses in tomato, including a completely new virus, which has a genome of ∼13.4 kb and groups with aphid-transmitted viruses in the genus Cytorhabdovirus. Although both DNA and RNA viruses can trigger the biogenesis of virus-derived small interfering RNAs (vsiRNAs), we show that features such as length distribution, paired distance, and base selection bias of vsiRNA sequences reflect different plant Dicer-like proteins and Argonautes involved in vsiRNA biogenesis. Collectively, this study offers insights into host-virus interaction in tomato and provides valuable information to facilitate the management of viral diseases. IMPORTANCE Tomato is an important source of micronutrients in the human diet and is extensively consumed around the world. Virus is among the major constraints on tomato production. Categorizing virus species that are capable of infecting tomato and understanding their diversity and evolution are challenging due to difficulties in detecting such fast-evolving biological entities. Here, we report the landscape of the tomato virome in China, the leading country in tomato production. We identified dozens of viruses present in tomato, including both well-documented and completely new viruses. Some newly emerged viruses in tomato were found to spread fast, and therefore, prompt attention is needed to control them. Moreover, we show that the virus genomes exhibit considerable degree of polymorphisms and recombination, and the virus-derived small interfering RNA (vsiRNA) sequences indicate distinct vsiRNA biogenesis mechanisms for different viruses. The Chinese tomato virome that we developed provides valuable information to facilitate the management of tomato viral diseases.

Fusion Protein Targeted Antiviral Peptides: Fragment-Based Drug Design (FBDD) Guided Rational Design of Dipeptides Against SARS-CoV-2

2020 ◽  
Vol 21 (10) ◽  
pp. 938-947
Author(s):  
Sounik Manna ◽  
Trinath Chowdhury ◽  
Piyush Baindara ◽  
Santi M. Mandal
Keyword(s):  
Public Health ◽  
Drug Design ◽  
Infectious Diseases ◽  
Fusion Protein ◽  
Fusion Process ◽  
Viral Fusion ◽  
Enveloped Viruses ◽  
Antiviral Peptides ◽  
Target Sites ◽  
Tract Infections

: Infectious diseases caused by viruses have become a serious public health issue in the recent past, including the current pandemic situation of COVID-19. Enveloped viruses are most commonly known to cause emerging and recurring infectious diseases. Viral and cell membrane fusion is the major key event in the case of enveloped viruses that is required for their entry into the cell. Viral fusion proteins play an important role in the fusion process and in infection establishment. Because of this, the fusion process targeting antivirals become an interest to fight against viral diseases caused by the enveloped virus. Lower respiratory tract infections casing viruses like influenza, respiratory syncytial virus (RSV), and severe acute respiratory syndrome coronavirus (SARS-CoV) are examples of such enveloped viruses that are at the top in public health issues. Here, we summarized the viral fusion protein targeted antiviral peptides along with their mechanism and specific design to combat the viral fusion process. The pandemic COVID-19, severe respiratory syndrome disease is an outbreak worldwide. There are no definitive drugs yet, but few are in on-going trials. Here, an approach of fragmentbased drug design (FBDD) methodology is used to identify the broad spectrum agent target to the conserved region of fusion protein of SARS CoV-2. Three dipeptides (DL, LQ and ID) were chosen from the library and designed by the systematic combination along with their possible modifications of amino acids to the target sites. Designed peptides were docked with targeted fusion protein after energy minimization. Results show strong and significant binding affinity (DL = -60.1 kcal/mol; LQ = - 62.8 kcal/mol; ID= -71.5 kcal/mol) during interaction. Anyone of the active peptides from the developed libraries may help to block the target sites competitively to successfully control COVID-19.

Biosecurity and Public Health Ethics Issues Raised by Biological Threats

2019 ◽  
pp. 773-785
Author(s):  
Nicholas Evans ◽  
Thomas Inglesby
Keyword(s):  
Public Health ◽  
Resource Allocation ◽  
Infectious Diseases ◽  
Ethical Issues ◽  
Emerging Infectious Diseases ◽  
Biological Weapon ◽  
Ethical Values ◽  
Dual Use ◽  
Health Concerns ◽  
Trade Offs

This chapter introduces ethical issues that arise in the context of biosecurity: policies and actions intended to prevent the development or emergence, or mitigate the consequences, of serious biological threats. These threats could include deliberate biological weapon attacks (bioterrorism), pandemics, emerging infectious diseases, or major laboratory accidents. The basic values that underpin these public health concerns are first introduced. Ethical issues that arise before, during, and following a biosecurity crisis are then examined, including issues of resource allocation, dual-use research, and the possibility of quarantine. Their resolution requires trade-offs among different ethical values, including utility, fairness, and liberty.

Communicable and Other Infectious Diseases

2020 ◽  
Author(s):  
Markus Frischhut
Keyword(s):  
Public Health ◽  
European Union ◽  
Infectious Diseases ◽  
Disease Transmission ◽  
Eu Law ◽  
The European Union ◽  
Ethical Perspective ◽  
Health Measures ◽  
Environment Agency ◽  
And Control

This chapter discusses the most important features of EU law on infectious diseases. Communicable diseases not only cross borders, they also often require measures that cross different areas of policy because of different vectors for disease transmission. The relevant EU law cannot be attributed to one sectoral policy only, and thus various EU agencies participate in protecting public health. The key agency is the European Centre for Disease Prevention and Control. Other important agencies include the European Environment Agency; European Food Safety Authority; and the Consumers, Health, Agriculture and Food Executive Agency. However, while integration at the EU level has facilitated protection of the public's health, it also has created potential conflicts among the different objectives of the European Union. The internal market promotes the free movement of products, but public health measures can require restrictions of trade. Other conflicts can arise if protective public health measures conflict with individual human rights. The chapter then considers risk assessment and the different tools of risk management used in dealing with the challenges of infectious diseases. It also turns to the external and ethical perspective and the role the European Union takes in global health.

scholarly journals Expanding U.S. Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole-Genome Sequencing through the CDC's Antibiotic Resistance Laboratory Network

2020 ◽  
Vol 58 (4) ◽  
Author(s):  
Ellen N. Kersh ◽  
Cau D. Pham ◽  
John R. Papp ◽  
Robert Myers ◽  
Richard Steece ◽  
...  
Keyword(s):  
Public Health ◽  
Antibiotic Resistance ◽  
Neisseria Gonorrhoeae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Whole Genome ◽  
Content Type ◽  
Laboratory Capacity

ABSTRACT U.S. gonorrhea rates are rising, and antibiotic-resistant Neisseria gonorrhoeae (AR-Ng) is an urgent public health threat. Since implementation of nucleic acid amplification tests for N. gonorrhoeae identification, the capacity for culturing N. gonorrhoeae in the United States has declined, along with the ability to perform culture-based antimicrobial susceptibility testing (AST). Yet AST is critical for detecting and monitoring AR-Ng. In 2016, the CDC established the Antibiotic Resistance Laboratory Network (AR Lab Network) to shore up the national capacity for detecting several resistance threats including N. gonorrhoeae. AR-Ng testing, a subactivity of the CDC’s AR Lab Network, is performed in a tiered network of approximately 35 local laboratories, four regional laboratories (state public health laboratories in Maryland, Tennessee, Texas, and Washington), and the CDC’s national reference laboratory. Local laboratories receive specimens from approximately 60 clinics associated with the Gonococcal Isolate Surveillance Project (GISP), enhanced GISP (eGISP), and the program Strengthening the U.S. Response to Resistant Gonorrhea (SURRG). They isolate and ship up to 20,000 isolates to regional laboratories for culture-based agar dilution AST with seven antibiotics and for whole-genome sequencing of up to 5,000 isolates. The CDC further examines concerning isolates and monitors genetic AR markers. During 2017 and 2018, the network tested 8,214 and 8,628 N. gonorrhoeae isolates, respectively, and the CDC received 531 and 646 concerning isolates and 605 and 3,159 sequences, respectively. In summary, the AR Lab Network supported the laboratory capacity for N. gonorrhoeae AST and associated genetic marker detection, expanding preexisting notification and analysis systems for resistance detection. Continued, robust AST and genomic capacity can help inform national public health monitoring and intervention.

scholarly journals Ocular manifestations of emerging viral diseases

Eye ◽  
2021 ◽  
Author(s):  
Ashwin Venkatesh ◽  
Ravi Patel ◽  
Simran Goyal ◽  
Timothy Rajaratnam ◽  
Anant Sharma ◽  
...  
Keyword(s):  
Public Health ◽  
Infectious Diseases ◽  
Influenza A ◽  
Emerging Infectious Diseases ◽  
Global Scale ◽  
Viral Diseases ◽  
Valley Fever ◽  
Ocular Manifestations ◽  
Influenza A H1n1 ◽  
Emerging Viral Diseases

AbstractEmerging infectious diseases (EIDs) are an increasing threat to public health on a global scale. In recent times, the most prominent outbreaks have constituted RNA viruses, spreading via droplets (COVID-19 and Influenza A H1N1), directly between humans (Ebola and Marburg), via arthropod vectors (Dengue, Zika, West Nile, Chikungunya, Crimean Congo) and zoonotically (Lassa fever, Nipah, Rift Valley fever, Hantaviruses). However, specific approved antiviral therapies and vaccine availability are scarce, and public health measures remain critical. Patients can present with a spectrum of ocular manifestations. Emerging infectious diseases should therefore be considered in the differential diagnosis of ocular inflammatory conditions in patients inhabiting or returning from endemic territories, and more general vigilance is advisable in the context of a global pandemic. Eye specialists are in a position to facilitate swift diagnosis, improve clinical outcomes, and contribute to wider public health efforts during outbreaks. This article reviews those emerging viral diseases associated with reports of ocular manifestations and summarizes details pertinent to practicing eye specialists.

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