key: cord-0716388-zubjxe8x authors: Raj, Pushker title: Classification of medically important viruses II: RNA viruses date: 1994-09-01 journal: Clinical Microbiology Newsletter DOI: 10.1016/0196-4399(94)90005-1 sha: a3921a5722bae0c58683e61be509ec6c00b84bd2 doc_id: 716388 cord_uid: zubjxe8x nan (i) Enterovirus---There are more than 72 members of the enterovirus genus that infect humans. The important ones are poliovims (types 1, 2, and 3), coxsackieviruses A (1 to 22, 24) and B (1 to 6), ECHO viruses (32 serotypes), new enterovirnses 68 to enterovirus 71, simian enteroviruses, and simian (18 serotypes), bovine (7 serotypes), and porcine (8 serotypes) enteroviruses. (ii) Rlfinovims---human rhinovimses (113 serotypes causing common colds), equine, and bovine rhinovimses. (iii) Cardiovirus----cncephalomyocarditis virus of mice (EMC), mengovirus of mouse, and ME virus of mouse. (iv) Aphthovims--Foot and mouth disease (FMD) virus types O and A (now termed as aphthovirus O and A) was the first animal virus isolated. (v) Heparnavirus----hepatitis A virus (human enterovirus 72). The family Caliciviridae is a newly described class of viruses that has been clearly separated from the Picomaviridae. The genus Calicivirus (from the Latin "calici," meaning cup-like) ineludes at least five distinct types that are found in the gastrointestinal tract of humans. The virion is similar to picornaviruses but slightly larger (37 nm). The genome is a single molecule of infectious, ss-RNA, positive-sense RNA with no lipid and no envelope. The Norwalk virus, a cause of acute gastroenteritis, has shown several similarities to calicivirus. Therefore, this agent has been classified as a probable calicivims. There are a number of sero-types belonging to the single genus of family Caliciviridae: Calicivirus--vesicular exanthema of swine virus (VESV), feline calicivirus (FCV) (formerly feline picornavirns), San Miguel sea lion virus (SMSV), and Norwalk virus. The members of the family reoviri, dae (Sigla: respiratory enteric o~) are medium-sized (60 to 80 nm), nonenveloped, ether-resistant viruses containing segmented ds-RNA. Reovimses (iii) Reovirus---The genome has 10 segments. It includes mammalian reoviruses (three serotypes), and avian reoviruses (five serotypes). (iv) Cypovirus Cytoplasmic polyhedrosis group of insect viruses. The members of this newly described family are nonenveloped medium-sized (60 nm) virions with bisegmented ds-RNA. There are no known human pathogens belonging to this family of viruses. There is only one genus: Birnavirus---Infectious pancreatic necrosis virus of fish, infectious bursal disease virus of chickens. The name of this virus family is derived from Latin word "toga," meaning gown (loose garment/envelope). Togaviruses include many of the viruses previously known as arboviruses (arthropod-borne) that are major human pathogens, as well as rubella virus. The virion are medium-sized (60 to 70 nm), enveloped, ether-sensitive with ss-RNA, positive-sense RNA. The virus particles mature by budding from the host cell plasma membrane. Five genera have been described: (i) Alphavirus--formedy arbovirus group A, it includes about 20 mosquitoborne viruses, all serologically related. The genus also includes Chikungunya, Sindbis, Semliki Forest virus, western equine encephalitis (WEE), eastern equine encephalitis (F~E), Venezuelan equine encephalitis (VEE), Ross fiver virus, and O'Nyong-Nyong. (ii) Rubivirus---rnbella virus (German measles). (iii) Pestivirus----bovine virus diarrhea (mucosal disease complex), hog cholera virus (European swine fever), and Border disease virus. (iv) Arterivirus--equine artefitis virus, simian hemorrhagic fever virus, Lelystad virus (porcine reproductive and respiratory syndrome virus), and VR2332. (v) Unclassifiet--Riley's lactate dehydrogenase-elevating virus (LDHV) of mice. The members of this newly established family flavivifidae (from the Latin "flavus," meaning yellow) include the viruses of the former genus Flavivirus of the Togaviridae family. The members of the family are enveloped viruses, slightly smaller than the Togaviruses (45 to 50 nm), containing ss, positive-sense RNA. The vifion matures within cistemae of the endoplasmic reticulum in contrast to the alphaviruses that mature at the plasma membrane. This group of arboviruses includes yellow fever virus. Most memhers are transmitted by blood-sucking arthropods. Two genera, flavivirus and hepatitis C virus (HCV), have been described: (i) Flavivirus---former arbovirus group B, about 50 viruses, all serologi-cally related. It includes mosquitoborne viruses of yellow fever, West Nile fever, Japanese encephalitis, dengue (four serotypes), Murray valley encephalitis, Kunjin, St. Louis encephalitis, tick-borne viruses of Omsk hemorrhagic fever, and Russian spring-summer encephalitis. (ii) Hepatitis C virus (HCV)---Recently described non-A, non-B hepatitis virus (NANBHV) that is transmitted by blood transfusions or sexual contact is now called hepatitis C virus (HCV). This virus has properties similar to those of flavivirus. The members of the family Arenaviridae (from the Latin "arenosus," meaning sandy; appearance of the virus particle by electron microscopy) are enveloped spherical or pleomorphic viruses ranging in size from 50 to 300 nm. The genome is ss-RNA that is negative-sense, i.e., complementary to mRNA. The virions incorporate host cell ribosomes during maturation, which gives the particles a "sandy" appearance. Most members of this family are unique to tropical America (i.e., the Tacaribe complex). All arenaviruses pathogenic for humans cause chronic infections in rodents. Lassa fever virus of Africa is one example. Only one genus has been described: Arenavirus--The type species is lymphocytic choriomeningitis viruses (LCM). This virus can establish persistent infections in mice and occasionally can cause aseptic meningitis in humans. Other members of the genus are the Lassa fever virus and members of the Tacafibe virus complex, including Junin virus (Argentine hemorrhagic fever), Machupo virus (Bolivian hemorrhagic fever), and Pichinde virus (nonpathogenic in humans). These viruses are highly contagious and fatal and are designated as "Biosafety level 4" pathogens. NOTE: No responsibility is aasumod by the Publisher for any injury and/or damag© to persons or proporty as a matter of products liability, n©gligoace or othcnvis¢, or from any use or operation of any methods, prodncts, instmctlons or idos contained in the material herein. No suggested teat or procedure should b¢ carried out unless, in the rosder's judgment, its risk is justified. Because of rapid advances in medical sciences, we recommend that the indcp©ndem v©fification of diagnoses and drag dosages should be made. Discussions, views, and rccommendatious as to rncdical procedores, choice of drugs, and drug dosages arc the respousibility ofth© authors. The relroviruses (from the Latin "retro," meaning backwards; reverse transcribes RNA to DNA) are enveloped viruses (90 to 120 nm) whose genome contains duplicate copies of high molecular weight, ss-RNA of the same polarity as viral mRNA. The virion contains a reverse transcriptase (RNA-DNA). The virus is replicated from an integrated "provirus" DNA copy in infected cells. The association of acquired immunodeficiency syndrome (AIDS) with retroviruses has been well recognized. Three subfamilies of Retroviridae have been described. (i) Oncovirinae (from the Greek "oncos," meaning tumor)--a large group, including members causing leukemias or sarcomas of animals and humans, some transduce cellular oncogenes. Mouse mammary tumor virus, human Tlymphotropic virus (HTLV-1, HTLV-2, HTLV-5), and Rous sarcoma virus (chickens). (ii) Lentivirinae (from the Latin "lenms," meaning slow)---slow disease onset, cytolytic, nononcogenic, cause neurological disorders. Human immunodeficiency virus (HIV-1, HIV-2), visna/maedi virus group (sheep), and caprine artheritis/encephalitis virus (goats). (iii) Spumavirinae (from the Latin "spuma," meaning foam)--foamy viruses of humans, not oncogenic, cause no clinical disease but characteristic vacuolated "foamy" cytopathology. The members of the orthomyxoviridae (from the Greek "orthos," meaning straight, true; and Greek "myxa," meaning mucus; affinity for mucins, glycoprotein cell surfaces) family are medium-sized, 80 to 120 run enveloped viruses containing a segmented ss-RNA, negative-sense RNA genome. Particles are either round or filamentous. As part of their surface, orthomyxoviruses have projections that contain hemagglutinin or neuraminidase activities. The internal nucleoprotein helix measures 9 to 15 nm, and the RNA is made up of eight segments. During replication, the nucleocapsid is assembled in the nucleus, whereas the hemagglutinin and neuraminidase accumulate in the cytoplasm. The virus matures by budding at the cell membrane. All orthomyxoviruses are influenza viruses that infect humans or animals. The segmented nature of the viral genome permits ready genetic reassortment when two influenza viruses infect the same cell; this explains the high rate of natural variation among influenza viruses. The influenza A virus has two specific surface antigens; hemagglutinin (H) and neuraminidase (N). There are 12 subtypes of H (HI to H12) and nine subtypes of N (N1 to N9). There are two genera of orthomyxoviruses: (i) Influenzavirus--type A (human, equine, and swine), type B, and swine plague; (ii) Influenzavirus C (only one strain) causes mild respiratory disease (7). The members of the family Paramyxoviridae (from the Greek "para,'" by side of; hemagglutinin and neuraminidase activities on the same polypeptide spike on the envelope) are similar to but larger (150 to 300 nm) than orthomyxoviruses. Both the nucleocapsid and the hemagglutinin are formed in the cytoplasm. Those infecting humans include mumps, measles, parainfluenza virus, and respiratory syncytial virus. In contrast to influenza viruses, paramyxoviruses are genetically stable. Three genera of paramyxoviruses have been described: (i) Paramyxovirus----parainfluenza type 1, 2, and 3 viruses of humans, parainfluenza virus of several animal species, mumps virus, Newcastle disease virus, Yucaipa, and other avian paramyxoviruses. (ii) Morbillivirus measles, canine distemper, and rinderpest. (iii) Pneumovirus--respiratory syncytial virus (RSV) of humans and cattle, and pneumonia virus of mice. The members of family Rhabdoviridae (from the Greek "rhabdos," meaning rod) are enveloped virion resembling a bullet, flat at one end and round at the other, measuring about 75 x 180 nm. The envelope has 10 nm spikes. The genome is ss, nonsegmented, negative-sense RNA. Particles are formed by budding from the cell membrane. The most lethal rabies virus belongs to this group. Two genera arc described: (i) Vesiculovirus (from the Latin "vesicula,'" meaning blister)---Vesicular stomatitis virus (VSV) with a wide host range and Chandipura virus. (ii) Lyssavims (from the Greek "lyssa," meaning rage; rabies)---rabies. The members of the family Filoviridae (from the Latin "fihm," meaning thread) are highly infectious, enveloped, pleomorphic virions. The diameter of the virion is 80 nm in diameter and has varying lengths ranging from 130 nm to 14,000 nm. The genome is negative-sense, ss-RNA. These viruses resemble rhabdoviruses in some aspects but have been grouped as a separate family on the basis of properties significantly different from those of established families. Replication occurs in the cytoplasm; assembly occurs by budding from the cell membrane. Only one genus has been established: Filovirus--including Marburg virus, a simian virus that is highly pathogenic for humans, and Ebola virus. Both these viruses cause hemorrhagic fever and are highly infectious. The members of the family Coronaviridae (from the Latin "corona," meaning crown; petal-shaped or clubshaped) are enveloped, 80 to 160 nm particles containing an unsegmented genome of ss-RNA; the nucleocapsid is probably helical, 11 to 13 nm in diameter. They resemble orthomyxovimses, but coronaviruses have petal-shaped surface projections arranged in a fringe like a solar corona. Coronavirus nucteocapsids develop in the cytoplasm and mature by budding into cytoplasmic vesicles. Human coronaviruses have been isolated from patients with acute upper respiratory tract infections. Coronaviruses of animals readily establish persistent infections. Only one genus has been described in this family: Coronavirus--members include avian infectious bronchitis virus, mouse hepatitis virus. The name of this family is derived from Bunyamwera, a location in Uganda, Africa, where the type species of virus was isolated. This is the largest virus family of the vertebrates with more than 225 members. The virion is a spherical, 90 to 100 om particle that replicates in the cytoplasm and acquires an envelope by budding into the Golgi apparatns. The genome is made up of a triple-segmented, ss, negative-sense RNA. The majority of these viruses are transmitted to vertebrates by arthropods (arboviruses). Hantaviruses, a cause of hemorrhagic fevers and nephropathy, are transmitted to humans by rodents. The Bunyaviridae have five genera: (i) Bunyavints---includes all former arbovirns group C viruses. 145 viruses, mosquito-transmitted; California encephalitis group including La Crosse, Lumbo, and Snowshoe hare virus, Bunyamwera supergroup. (ii) Phlebovirus---sandfly (Phlebotomus) fever, Rift Valley fever. These are predominantly sandfly-borne viruses. (iii) Nairovims---4ick-tran sm itted; Crimean-Congo hemorrhagic fever (CCHF--two serotypes), Nairobi sheep disease. ( A virus is a set of genes, either DNA or RNA, packaged in a protein-containing coat. The extracellular infectious virus particle is called a virion. There are certain viruses that have insufficient information to permit classification. Re-cently, unconventional virus-like forms of life have been discovered that have entirely different properties. These forms have been termed as vimids and prions. The term '~iroids" has been introduced for a new class of subviral agents characterized by the apparent absence of an extracellular dormant phase (virion) and by a genome much smaller than those of known viruses. Viroids are infectious, low molecular weight circular RNA molecules that lack protein shells (capsid) and are resistant to heat and organic solvents but sensitive to nucleases and are responsible for a variety of plant diseases. The name "prices" has been proposed for another new class of proteinaceous infectious particles that lack any detectable nucleic acid. Prions are resistant to heat, UV rays, and nucleases, but are sensitive to proteases and they seem to be nonimmunogeneic. These are transmissible infectious agents responsible for some viral diseases with very long incubation periods (up to 30 years in humans), including neurodegenerative disorders such as kuru; Creutzfeldt-Jakob disease (CJD) (small particles probably 4 to 6 nm in diameter; Gerslmann-Stranssler-Scheinker disease (GSS); the animal diseases scrapie of sheep and goats, bovine spongiform encephalopathy, chronic wasting diseases of mule deer and elk, and transmissible mink encephalopathy. This group of agents is also known as the chronic infections neuropathic agents (CHINA viruses). Delta hepatitis or hepatitis D virus (HDV) is a defective satellite of hepatitis B virus, requiring the presence of hepatitis B virus for its replication and assembly. The virion is 35 to 37 nm in diameter and consists of an envelope made of HBsAg surrounding a s~ containing delta antigen. The infections caused by this agent may be acute or chronic. Recently, a 32-to 42-nm spherical non-A, non-B hepatitis virus (NANBHV) that is responsible for waterborue epidemics in developing countries, has been named as hepatitis E virus (HEV). On the basis of physicochemical characterization and morphological properties, HEV resembles calicivirus (2) , but genomic analysis indicates similarities to Alphavirus (5, 10) . Further characterization is needed for the final taxonomic classification. The name Toroviridae has been proposed for the undescribed douglmub shaped, ss-RNA viruses associated with diarrhea in horses (Berne virus) and calves (Breda virus). RNA-containing Borna disease virus causes an encephalomyelitis of horses and sheep. These are not fully characterized and are unclassified. Astrovirus has been visualized by electron microscopy in fecal specimens from humans, calves, dogs, swine, ducks, turkeys, and lambs. At present five antigenically distinct groups of human astrovirus have been described. The virions are spherical, 27 to 32 nm in diameter, and have a characteristic star-shaped appearance. Their genome consists of ss RNA about the same size as that of picornaviruses. Arbovimses (Sigla: arthropodhome) do not belong to a virus family. These are the viruses that are pathogenic for humans and are arthropodtransmitted. All of these viruses (>350) have a complex cycle involving arthropods as vectors that transmit the viruses to vertebrate hosts by their bite. Virus replication does not seem to harm the infected arthropod. Arboviruses infect humans, mammals, birds, and snakes and use mosquitoes and ticks as vectors. Human pathogens include dengue, yellow fever, encephalitis viruses, and others. Arboviruses belong to several virus families, including Togaviridae, Flaviviridae, Bunyaviridae, Rhabdoviridae, Arenaviridae, and Reoviridae. The information on the taxonomic classification of medically important animal viruses is very helpful in microbiological diagnostic laboratories, in medicine, in teaching, in research, and in veterinary medicine. It is the continuous work of the members of the ICI~ who gathered this information over a long period of time that has improved our understanding of viral diseases. With the existing knowledge, the diagnosis of most viral diseases is much simplified either by isolating the viruses in culture, or by serological or immunological tests, or molecular biology approaches. Classification of the medically important viruses: DNA viruses Etiological agent of enterically transmitted non-A, non-B hepatitis Emerging infectious diseases: Hantavirus Pulmonary Syndrome, United States Biological concepts in virus classification Computer-assisted assignment of functional domains in the non-structural polyprotein of hepatitis E virus: delineation of a new group of animal and plant positivestrand RNA viruses Structure and classification of viruses Classification and nomenclature of viruses. Fourth Report of the International Committee on Taxonomy of Viruses Structure and classification of viruses Virus taxonomy Hepatitis E virus (HEV): molecular cloning and sequencing of the full-length viral genome Editorial Veterinary Antimicrobial Susceptibility Testing Coming of Age Joel E. Mortensen, Ph.D. Director of Microbiology St. Christopher's Hospital for Children Philade~Thia Clinical microbiology laboratories in hospitals, clinics, or private settings are accustomed to handling bacterial pathogens from humans, conducting standardized antimierobial susceptibility testing (AST), and reporting results to physicians. On the other hand, veterinary AST (VAST) is conducted by a variety of laboratories ranging from the large state-of-the-art (university, state, or private) to a practitioner's back offlee; all without accepted guidelines or standards. It has been the custom for the more proficient laboratories to follow the existing National Committee for Lalxr-ratt~ Standards (NCCL~) standards, but each may use different modifications of these ~ocedmes to accommodate the fastidious pathogens associated with veterinary bacteriology. In addition to the discrepancies of media and methods, the only source of interpretive criteria for determining the susceptibility of vetexinary pathogens has been developed using human pathogens, pharmacokinetics, and clinical trials. These extrapolated criteria have led to some confusion when veterinary laboratory results are applied in actual clinical veterinary practice.To address this situation the NCCLS Area Committee on Microbiology has recently formed a subcommittee (NCCLS Subcommittee on Veterinary Antimicrobial Susceptibility Testing) to address the unique needs of laboratories and clinicians dealing with antimicrobial susceptibility testing of bacteria from cattle, swine, poultry, horses, dogs, and lactating dairy cattle. The subcommittee was formed in 1993 and comprises representatives from the animal health industry, university laboratory diagnosticians, test equipment manufactm'ers, government regulatory officials, veterinarY.% and members of the human use AST committee. The VAST subcommittee is charged with the task of developing standards for the performance of AST and rational interpretive criteria for specific antibiotics and animal species, and assisting government and animal health industry regulatory groups in developing the testing criteria for new as well as for existing antimicrobial agents.The fast step taken by the subcommittee was to develop methodological standards for VAST. It was decided to use the current NCCLS documents for easily grown aerobic Imlhogens such as gram-negative organisms (e.g., pasteurellae, entcrics) and gnun-positive organisms (e.g., staphylococci and streptococci) as a starting point in developing a tentative document of specific veterinary standards (1, 2) . In addition, current working groups are addressing standardization of media and conditions for the growth of fastidious pathogens such as Actinobacillus pleuropneumoniae (swine respiratory pathogen) and Haemophilus somnus (cattle pathogen). Anaerobic microorganisms, mycobacteria, mycoplasma, spirochetes, and agents of minor disease concern have been intentionally excluded at this time. Quality control organisms and antimierobial agents used in both human and veterinary medicine are accepted by the subcommittee (e.g., penicillins, erythromycin, tetracycline, tested with American Type Culture Collection strains);