Eastern equine encephalitis virus

This chapter reviews various diagnostic tests available for central nervous system (CNS) infections and provides a detailed discussion of specific molecular approaches to the most common organisms causing meningitis and encephalitis in the United States. A vast array of organisms have been associated with encephalitis, including bacteria, fungi, viruses, and protozoa. Just as meningitis and encephalitis localize to distinct compartments of the CNS, the pathogens causing these two syndromes differ, and the respective microbiologies of meningitis and encephalitis are discussed separately. While the chapter focuses on the use of molecular assays for diagnosis of CNS infection, traditional microbiological diagnostic approaches continue to play an important role in pathogen identification and are complementary to nucleic acid amplification techniques. A DNA probe array has been developed for the simultaneous identification of herpesviruses, enteroviruses, and flaviviruses after several PCR amplifications. Nucleic acid amplification techniques have markedly improved the identification of CNS infections caused by viral and fastidious bacterial pathogens. Molecular techniques such as PCR allow rapid diagnosis, with consequent improvement of outcomes and cost savings. Results of molecular diagnostic testing for CNS infections must be interpreted in the context of the individual patient presentation and clinical illness, and close cooperation between the laboratory and the clinician is required for optimal use of these technologies.

Viruses exhibit an extremely high mutation rate relative to their hosts, and are constantly changing genetically, with the consequence that their host range is in constant flux. Viruses are important vectors for vaccines against viral pathogens and nonviral pathogens and neoplasia. The plan of coordinated gene expression is based on genome replication, and viral genes can be classified as early (pre-genome replication) versus late (post-genome replication). The replication of RNA viruses results in the presence of unusually high amounts of double-stranded RNA in the cytoplasm. Viral replication of hepatocytes appears to be innocuous, with the damage coming over many years from virus-specific CD8+ T-cells that infiltrate the liver and destroy infected cells. The innate immune system has nearly complete responsibility for controlling infections for the first 3 to 5 days after infection with an infectious agent that the host has not previously experienced. Perhaps this is sufficient to completely contain low-level infections with some viruses, but for more serious threats the adaptive immune system must be mobilized to contain and clear the infection. The adaptive immune system has a variety of effector mechanisms for this purpose, all based on the specificity of antibodies and T-cell receptors for viral antigens. The genes encoding these remarkable molecules are the only genes in vertebrates that are routinely subject to somatic mutation and rearrangement. This enables the immune system to keep pace with genetic variability of viruses (and other pathogens), maintaining the capacity to respond specifically to virtually any virusencoded protein.

The alphaviruses are principally mosquito-borne, positive-strand RNA viruses in the family Togaviridae that exhibit a broad range of pathogenicity in humans and animals. The replication complexes of alphaviruses are associated with cytoplasmic membranes, and the main determinant of membrane attachment seems to be nsP1, which is hydrophobically modified by palmitoylation of cysteine residues. In humans, an age-dependent susceptibility of infants and the elderly to central nervous system (CNS) infection has been observed epidemiologically, although its pathogenesis has not been elucidated. Immature mouse neurons infected with Sindbis Virus (SINV) or Semliki Forest Virus (SFV) die of caspase-dependent apoptosis, while mature neurons survive by producing factors inhibiting virus-induced apoptosis. Apoptosis is induced at the time of alphavirus fusion with the cell membrane, and virus replication is not required. Mayaro virus (MAYV) is the principal New World representative of alphaviruses within the SFV complex. The epidemiological pattern is explained by the forest cycle of viral transmission, probably between Hemagogus mosquitoes and wild vertebrates, including monkeys and marmosets, analogous to the sylvatic cycle of yellow fever. The majority of infections with the arthritogenic alphaviruses are benign but temporarily debilitating. Barmah Forest virus (BFV), named after the site in northern Victoria where it was first isolated from Culex annulirostris mosquitoes, is antigenically distinct from other alphaviruses, including River virus (RRV) and SINV, that are also found in Australia. Alphaviruses principally are maintained in zoonotic transmission cycles in natural habitats.

Microbial source tracking (MST), the determination of a source of microorganisms into an environment, is a phrase that has been used by various microbiology disciplines. This chapter discusses some of the research and development efforts in bio-forensic technologies underway in the Department of Homeland Security (DHS) Science and Technology Directorate. The chapter provides examples of some outbreaks that occurred and the responses by various relevant groups. A number of natural disease outbreaks have tested the readiness of the health care and political communities to respond and quickly and effectively manage them. A few recent outbreaks that can serve as examples are those of Sin Nombre hantavirus pulmonary syndrome, West Nile disease, severe acute respiratory syndrome (SARS), United Kingdom foot-and-mouth disease, Asian soybean rust, and avian influenza. Anthrax is caused by the gram-positive endospore-forming bacterium Bacillus anthracis. It has a long history as a human pathogen, and several authorities speculate that it was the cause of the sixth Egyptian plague recorded in the book of Genesis. There is opportunity for all those interested ultimately in human health safety, whether they are directly involved in issues related to human disease, plant disease, animal disease, water quality, air quality, soil quality, or food safety, to join their resources. It is the combined knowledge of these fields that will allow the most efficient approach for national security.

This chapter provides practical guidance to facilitate compliance with current national and international regulations that govern the packing and shipping of hazardous materials and dangerous goods. Topics in this chapter include terminology, classification and naming of diagnostic specimens and infectious substances, marking and labeling packages, packaging material, documentation, training and certification of personnel, practical suggestions for classifying diagnostic specimens and infectious substances, and resources for additional information. Medical waste which is reasonably believed to have a low probability of containing infectious substances must be packed and shipped as Medical Waste. Department of Transportation (DOT) regulations, International Air Transport Association (IATA) requirements, and IATA packing instructions (PI) describe the minimum standards for the safe transport of various biological materials. The marking and labeling on the outer container communicate essential information regarding the shipper and consignee of the package, the nature and weight of the contents of the package, the potential hazard of the substance, how the substance is packed, and information to be used in case of an emergency. There are several simple but extremely important points which must be regularly and strongly emphasized to persons who pack and ship diagnostic specimens and infectious substances.

Domesticated mammals include dogs, cats, cattle, sheep, goats, pigs, horses, donkeys, and camels. Agents are acquired from domestic animals by contact, ingestion, inhalation, or inoculation. Some agents are host specific and do not readily cross species, in particular, some zoonotic viruses. Other agents have a broader host range, for instance, Lyssavirus, Brucella, Francisella, Salmonella, microsporidia, and Toxoplasma. In rare instances of species jumps from mammals to receptive humans, severe (virgin territory) epidemics can result. Examples include human immunodeficiency virus, Henipavirus, and severe acute respiratory syndrome-associated coronavirus. This chapter talks about the various types of infections spread by dogs, cats, domestic bovids, suids, equids, and camelids.

This chapter focuses on wild vertebrates which include carnivores, rodents, lagomorphs, primates, bats, birds, fish, reptiles and amphibians. Global trade, hunting safaris, sileage feeding, and habitat reduction increase chances of encounters with wild vertebrates, infections that cross from wildlife to livestock (e.g., Mycobacterium bovis), and jumps of agents across species to humans, e.g., human immunodeficiency virus (from primates in Africa), monkeypox virus (from Gambian giant rats imported into the United States), and severe acute respiratory syndrome coronavirus (SARS-CoV) (from carnivores in China). By habitat and invertebrate vector, wild herbivores maintain zoonotic viruses, bacteria, and protozoa. In the African rain forest, hunters handling dead duikers (Cephalophus, a small forest herbivore) are suspected of triggering infection chains and outbreaks. In Africa and Southwest Asia, hyraxes (Procavia and Heterohyrax) are natural hosts of Leishmania aethiopica. Transmissible mink encephalopathy is sporadically diagnosed in farmed mink (Mustela vison). Seroreactivity in carnivores may merely reflect past exposure to arthropod-borne viruses. Skunks, weasles, raccoons, and red and gray foxes are presumed reservoir hosts of Powassan virus. Cryptosporidium muris infects mice and other rodents. Viruses reported in laboratory rodents include cytomegalovirus and ectromelia virus. Rodents in Africa, including squirrels (Funisciurus and Heliosciurus) and Gambian rats (Cricetomys emini), are likely reservoirs of Monkeypox virus (MPXV). The mammalian order Lagomorpha includes hares and rabbits (Leporidae) and pikas (Ochotonidae). Bordetella bronchiseptica and Pasteurella multocida commonly colonize the upper respiratory tract of laboratory and wild lagomorphs. Infections in humans can result from handling living or dead animals.

This chapter describes the host-parasite relationships in animals with microsporidiosis and how they relate to microsporidian infections in humans. The majority of immunologically competent hosts who became infected with microsporidia (e.g., rabbits and mice) developed chronic and persistent infections with few clinical signs of disease. At least three levels or stages of defense mechanisms are expressed to prevent or control infection with most microorganisms. These are innate resistance, early induced responses, and adapted immune responses. The majority of the microsporidian spores appeared to be destroyed after phagocytosis, although some microsporidia taken up by phagocytosis had extruded their polar filaments into the cytoplasm of the macrophage. Microsporidia that infect mammals often persist in the face of innate resistance, early induced response, and adapted immune response mechanisms. The clinical manifestations of microsporidiosis in animals, however, have been highly predictive of the disease in humans, and a competent immune system has been shown to be important in preventing lethal disease. A balanced host-parasite relationship developed in many animals with microsporidiosis that displayed few clinical signs of disease yet carried persistent infections. A better understanding of the immune responses that establish a balanced host-parasite relationship in animals will likely prove beneficial in understanding the immunology of microsporidiosis in humans and in developing immunotherapeutic and chemotherapeutic strategies that can be applied to microsporidiosis.