Positivesense Rna Viruses

There are six families of RNA viruses that contain a single-stranded genomic RNA molecule of message-sense. The genomic nucleic acid of positive-sense RNA viruses is fully infectious when delivered to cells in the absence of viral proteins. The gene expression strategies of these agents fall into three groups. The least complex is illustrated by the picornaviruses and flaviviruses. These agents have a single large open reading frame that encodes a single large polyprotein that is subsequently...

References

Expression of animal virus genomes. Bacteriol Rev 1971 35 235-241. 2. Mayo MA, Pringle CR. Virus taxonomy-1997. J Gen Virol 1998 79 (Pt 4) 649-657. 3. MHV van Regenmortel, Fauquet CM, Bishop DHL, Carstens EB, Estes MK, Lemon SM, Maniloff J, Mayo MA, McGeoch DJ, Pringle CR, Wickner RB. Virus Taxonomy The Classification and Nomenclature of Viruses. The Seventh Report of the International Committee on Taxonomy of Viruses. Vol. Vllth report of the ICTV. San Diego Academic Press, 2000....

Export of Etiologic Agents of Humans Animals Plants and related materials

Department of Commerce (DOC). 15 CFR Parts 730 to 799 This regulation requires that exporters of a wide variety of etiologic agents of human, plant and animal diseases, including genetic material and products that might be used for culturing large amounts of agents, obtain an export license. Information may be obtained by calling the DOC Bureau of Export Administration at (202) 482-4811 or through the Internet at http bxa.fedworld.gov or http www.bxa.doc.gov The CDC website provides...

Polymorphism typing

The basic premise of this technology revolves around using restriction enzymes to digest a DNA sample into fragments and to separate the resulting fragments by size by electrophoresis to produce a characteristic pattern or fingerprint. This pattern varies based on the number of times the enzyme recognition sequence occurs in the target DNA sequence and or the number of intervening repetitive sequences contained within a generated fragment. Restriction fragment length polymorphism (RFLP)...

Safety issues

The Centers for Disease Control Laboratory Response Network to Bioterrorism (LRN) recommends that samples to be analyzed for biological threat agents be processed within a certified Class II biological safety cabinet (BSC). Most diagnostic procedures deal with hydrated samples such as tissues and bodily fluids, and many biological samples from the environment are also hydrated, e.g., air collector fluids, water washings, etc. By the nature of such samples, procedures and protective equipment...

Protein Signature Pipeline

With straightforward extensions, the techniques above for nucleic acid detection diagnostics can be applied to protein sequences. When multiple pro-teomes are available from different strains or isolates, we perform a multiple sequence alignment on each protein to determine a protein consensus, using DIALIGN. These are compared using Vmatch against the GenBank nonredundant protein database, nr. This output is analyzed for apparently unique pep-tides of a given length (six or more amino acids,...

Epidemiologic Investigation for Public Health Biodefense and Forensic Microbiology

Bioterrorism Preparedness and Response Program, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia Division of Parasitic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia Microorganisms are very efficient at infecting humans, using a number of different strategies and mechanisms. The deliberate dissemination of a biological agent by many of these same mechanisms presents the latest...

Investigation Of Crop Disease Outbreaks

As with other outbreaks, it is necessary to have a clear understanding of what naturally occurring disease looks like in order to appreciate the unusual. An excellent review of natural plant diseases was given by Rogers 62 for convenience, the major points of that paper are summarized here. Just as in human or animal illness, crop diseases have typical epidemic curves depending on the interaction of the pathogen and its host. Plant pathogens that undergo one life-cycle in one crop growing...

Case Study Of Bacillus Anthracis

In this section, we will present some quantitative considerations related to microbial forensics. We will use published research on Bacillus anthracis to illustrate several important issues. We do so because the anthrax terrorist attacks of October 2001 have received considerable attention and, thus, offer concrete data for discussion. However, we will gloss over certain complications of this particular example in order to emphasize more general issues that would probably apply to similar cases...

The Immune Response

The immune system typically recognizes the invading pathogen at the site of entry, where it launches a generalized innate immune response. Signal molecules recruit inflammatory cells to the area which engulf cell debris and released virions. Virus proteins are presented to the adaptive immune system in local lymph nodes, allowing the host to create a directed defense against the virus. Effector T cells specific for virus antigen stimulate B cells to secrete virus-specific antibodies. There are...

West Nile

Microbial Forensics

The West Nile virus outbreak illustrates several important points. First, it illustrates the difficulty in identifying a virus, especially one that had never been seen before in the U.S. Second, it shows that even with an initial misidentifi-cation, state and federal agencies were still able to act effectively, knowing how similar viruses could be controlled. And last, this case illustrates that virus distribution can be tracked by monitoring those infected as well as its vector. In late August...

Multisequence And Multigenome Alignment

Another subject infrequently addressed for long sequences, and needing more in-depth exploration, is the issue of multiple alignments. Every alignment is based on a colinear arrangement of sequence similarities (e.g., the order of segments of similar sequence is preserved, although the distances between those segments may vary among the inputs). Therefore, a global alignment of whole genomes makes sense only if the species are closely related (or more precisely, if very few genome...

Tools For Protein Structure Modeling

The structures of over 8,000 proteins have been experimentally determined and are available in the Protein Data Bank (PDB) (http www.rcsb.org pdb ), but these are only a tiny fraction (less than 1 ) of all proteins that exist in nature. Determination of protein structures via X-ray crystallography or nuclear magnetic resonance imaging is a relatively slow and expensive process. Unlike genomic sequencing, which has seen several orders of magnitude of increase over the past several years, protein...

Sample scanning stage

FIGURE 13.8 Schematic illustration of confocal microscope used for the micro-Raman experiments. (a) The 488-nm line of an Ar+ laser is focused onto the sample with a high numerical aperture (NA) objective. The sample is mounted on an xy-piezo stage and raster-scanned over the focused laser beam. Raman scatter is collected with the same high-NA objective and focused onto a confocal aperture. The Rayleigh scatter is removed with a holographic notch filter, and the remaining Raman scatter is...

Melioidosis and Glanders

The pathogens responsible for melioidosis (Burkholderia pseudomallei) and glanders (B. mallei) are two closely related species. In fact, recent molecular analysis appears to indicate that B. mallei is a clonal derivative of the much more diverse B. pseudomallei. Both are Gram-negative aerobic rods, but cause very different diseases. Glanders is now an uncommon disease of horses and donkeys. Its natural occurrence is restricted to the Indian subcontinent, Africa, some Middle Eastern countries,...

Introduction

They prey on all forms of life from archaea and eubacteria to fungi, plants, and animals. It has been estimated that viruses that target sea-dwelling organisms, such as algae, turn over half of the world's biomass each day. As such, viruses are an important part of the ecological balance on earth. Of the vast collection of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) viruses, research has focused on the tiny fraction that cause disease in humans,...

Personnel

Laboratory Personnel Should Have the Education, Training, and Experience Necessary to Perform Examinations and Provide Testimony. The Laboratory Should 5.1.1. Have Written Job Description(s) for Personnel that Include Responsibilities, Duties, and Required Skills 5.1.2. Have a Documented Training Program for Assuring the Competence of All Technical Laboratory Personnel 5.1.3. Have a Documented Program to Ensure Technical Qualifications Are Maintained Through Continuing Education 5.1.3.1....

Igs Its Lsu Ssu 58s

FIGURE 6.7 Levels of taxonomic resolution provided by nucleotide sequence data of nuclear ribosomal DNA (rDNA) genes. IGS, intergenic spacer region ITS, internal transcribed spacer regions (ITS1 and ITS2) LSU, 28S large ribosomal subunit gene 5.8S ribosomal subunit gene and SSU, 18S small ribosomal subunit gene. Figure kindly provided by R. Vilgalys, Department of Biology, Duke University. FIGURE 6.7 Levels of taxonomic resolution provided by nucleotide sequence data of nuclear ribosomal DNA...

Sites for Virus isolation

The types of samples and the manner of collection depend upon the capabilities of the diagnostic laboratory. The chance of obtaining an active virus sample depends on many factors. The virus concentration varies in the body over the course of infection and may actually not be present when symptoms bring the patient to medical attention. The virus may have been cleared from the area of disease, or the symptoms may reflect damage induced by the immune system rather than direct virus pathology. It...

Contributors

Numbers in parentheses indicate the pages on which the author's contribution begins. graham bench (251), Center for Accelerator Mass Spectrometry, Energy and Environment Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551 roger g. breeze (1, 27), Centaur Science Group, Washington, DC 20007 bruce budowle (1), Federal Bureau of Investigation, Laboratory Division, Quantico, Virginia 22135 james p burans (1), National Bioforensic Analysis Center, Department of Homeland...

Multilocus Sequence Typing

As mentioned, comparing the complete sequence of entire genomes will reveal any and all genetic differences between the organisms compared. Mul-tilocus sequence typing (MLST) is a technique that can be used to compare microorganisms based on the DNA sequence of a set of genes rather than a single gene. This technique is usually used to compare microorganisms based on the sequences of conserved housekeeping genes (i.e., genes that are always expressed in the organism because they are essential...

Info

With SARS worldwide, the number of samples requiring diagnostics grew. Designation of SARS-CoV as a biosafety level 3 virus required specialized laboratories, so the WHO coordinated diagnostic labs from nine countries to work together to standardize diagnostic assays, supply similar reagents, ensure proper equipment availability, and analyze results in a comparable manner. Communication was vital with daily teleconferences, secure web sites, and exchange of patient samples and autopsy...

Examples Of Naturally Emerging Viruses

In May 1993, a clinician reported a cluster of cases presenting with nonspecific illness, fever, headache, and cough that rapidly progressed to respiratory distress. The patients were young, previously healthy, and lived in rural areas in the four-corners region bordering Arizona, Colorado, New Mexico, and Utah. By early June 1993, 24 cases had been reported with a mortality rate approximately 75 .11,12 Patient blood and autopsy tissues were sent to the Centers for Disease Control (CDC) for...

Investigation of Suspicious Disease Outbreaks

Department of Agriculture, Food Safety and Inspection Service, Office of Public Health Science, Athens, Georgia Centaur Science Group, Washington, DC Most of the terrorism experienced globally has involved highly localized attacks with explosives or toxic chemicals that produce mass casualties at the time of the event or soon after. Such incidents are obvious, and the extent of the damage can be readily and immediately perceived. This chapter is dedicated to investigation of covert attacks...

Dynamics Of Disease Transmission

Disease has been classically described as the result of an epidemiological triad, where disease results from the interaction of the human host, an infectious agent or toxin, and the environment that promotes the exposure.1 In some instances, an arthropod vector such as a mosquito or tick is involved. Among the assumptions necessary for this interaction to take place is that there is a susceptible host. The susceptibility of the host is influenced by a variety of factors including genetic,...

Growth Habit And Reproduction

Asexual Fungi Fruiting Bodies Acervulus

The life cycle of a fungus can vary considerably among species with respect to growth habit and reproduction. In general, most fungi produce some type of asexual and or sexual spore during their life cycle that enables them to grow, be disseminated, and or survive. Under favorable environmental conditions, spores germinate to produce a thread-like filament called a primary hypha (plural, hyphae) or germ tube. Hyphae grow by extension at the hyphal tips in a branching pattern that allows maximum...

Raman Spectroscopy and Surface Enhanced Raman Spectroscopy

Raman scattering is the inelastic scattering of photons off of molecular bonds. The Raman scattered photons differ in frequency from the incident and elas-tically scattered photons by the frequency of the molecular bond vibration. Figure 13.7 shows an energy level diagram illustrating the Raman scattering process. Most of the incident light is elastically scattered (Rayleigh scattered) however, a small fraction of the incident light ( 1 in 108 photons) is Raman scattered. Although the Raman...

Global Information Systems Tools to Assist Disease mapping

Many commercial software packages, referred to as Geographical Information Systems (GISs), allow display and manipulation of geo-referenced data52-54 useful in outbreak investigation. Most mapping programs allow construction of multiple map layers with different information in each layer. Two common software packages are Maplnfo at http www.mapinfo.com and ArcView at http www.esri.com software arcview. Other programs available as shareware (at the time of writing) include BUGS and BEAM at http...

History

The use of pathogenic agents as weapons has been documented for more than two millennia. The ancient Romans carried out biological warfare by putting carrion into the wells of their enemies to poison the water supply Such crude biowarfare tactics continued well into the 20th century.3'4 During the 14th-century siege of Kaffa (now Feodossia, Ukraine), the attacking Tartar soldiers experienced an epidemic of bubonic plague. The Tartars capitalized on the devastating disease and used the bodies of...

Epidemiology of intentional Botulism and differential diagnosis

The intentional release of botulism is most likely to be associated with the outbreak of a large number of cases of flaccid paralysis with prominent bulbar palsies. Other features may include an outbreak with an unusual toxin type (C, D, F or G, vide infra), an outbreak with common geographic features but without a common dietary exposure, or multiple simultaneous outbreaks with no common source. The incubation period for intentional botulism is unknown, but is likely related to the route of...

An Overview Of Microbial Diagnostics

The goal of bioinformatics in microbial forensics and diagnostics is to support the rapid identification of microbial samples at a variety of levels of resolution (family, species, strain, isolate). Techniques to accomplish this are ultimately based upon accurate determination and comparison of genomic sequence of high quality, combined with detailed analysis of the sequence to determine gene composition, protein structure, and the functional organization of the mechanisms of transmission and...

Scanning Electron Microscopy with Energy Dispersive Xray Microanalysis

SEM is a standard workhorse technique for characterizing particulate samples, found in many laboratories worldwide. It provides excellent imaging of the surfaces of agent particles and other material in a sample, and is an excellent initial technique to be applied for identifying likely agent particles for analysis by other instruments. When combined with EDX, the elemental composition of the material in the imaged region can be determined. Surface characterization and imaging of the various...

Viral Forensics the Schmidt Case

The value of phylogenetic analyses in forensics is well illustrated by the recent and curious criminal case of the State of Louisiana versus Richard J. Schmidt.50 The uncontested facts in this case are that a gastroenterologist from Lafayette, Louisiana broke into the home of his former mistress and office nurse late at night on August 4, 1994, and that he argued with her and gave her an intramuscular injection. He claimed it was a vitamin B shot. She claimed it was HIV She had begun feeling...

Foreword

Kilmacthomas is a small town of some 7,500 inhabitants, not far from Waterford in southern Ireland. In November 2001, the citizens of Kilmacthomas found themselves subject to the same fears that swept communities from Washington, D.C., to Nairobi, Karachi, Beijing, and thousands of other cities, towns and villages across the world. The Waterford News amp Star reported, together with the results of the whist drive in Ballylaneen, that the Kilmacthomas post office had been closed after a white...

Biological and physical integrity of a sample

Factors affecting biological integrity of agents samples may be highly variable because of the diverse array of threat agent characteristics, environmental conditions, sample matrices, agent concentrations, adversary threat-agent preparation methods, and methods used in sample collection and transport. With respect to threat agent characteristics, agents range from labile protein toxins to stable mycotoxins, from labile RNA viruses to stable poxviruses, and from fastidious bacteria to very...

Us Disease Surveillance And Reporting Systems

The Centers for Disease Control and Prevention CDC receives weekly mortality reports from 122 U.S. cities and metropolitan areas these summarize the total number of deaths occurring each week, as well as the number due to pneumonia and influenza. Reports are published in the Morbidity and Mortality Weekly Report MMWR at http www. cdc.gov epo dphsi phs.htm 121. The National Notifiable Diseases Surveillance System NNDSS , maintained by the CDC Epidemiology Program Office, is a mechanism for...

Keim P. Microbial Forensics A Scientific Assessment. A Report From American Academy Of Microbiology. Washington Dc 2002

Bioterrorism From threat to reality. Ann Rev Microbiol 2002 56 167-185. 2. Pearson GS. The threat of deliberate disease in the 21st century. Henry L Stimson Center Report, No. 24. Washington, DC Stimson Center 1998. 3. Christopher GW, Cieslak TJ, Pavlin JA, Eitzen EM. Biological warfare A historical perspective. JAMA 1997 278 412-417. 4. Stockholm International Peace Research Institute SPIRI . The Rise of CB Weapons The Problem of Chemical and Biological Warfare. New York, NY...

Forensic Case Examples

To better plan for forensic investigation strategies of an event, capitalizing on past experiences can shed light on current practices and the direction of future research. Two illustrative examples, neither of them bioterrorism acts, are the Sverdlovsk anthrax incident and the case of a dentist with AIDS who may have infected patients with HIV Both required epidemiological investigation and molecular biology to resolve. The first case explores the sources of anthrax spores from an anthrax...

Swgmgf

Since the first two components that the national microbial forensic laboratory will rely upon are addressed in other chapters, the focus here will be on the SWGMGF. The newly formed SWGMGF is hosted by the FBI and has a membership drawn from a wide range of federal agencies, as well as academia. Input from the private sector will be sought on a routine basis. As mentioned above, the SWGMGF is modeled after the successful practices in the human DNA forensic arena i.e., SWGDAM 30 which utilizes...