Welcoming you for any type of article submission for the upcoming issue on/before February 26, 2021.


Review Article
Volume 2 Issue 1 - 2016
The Practice of Clinical Virology: Virus Taxonomy
Lynne M Webber
Department of Medical Virology, University of Pretoria, South Africa
*Corresponding Author: Lynne M Webber, Department of Medical Virology, University of Pretoria, South Africa.
Received: January 22, 2016; Published: February 16, 2016
Citation: Lynne M Webber. “The Practice of Clinical Virology: Virus Taxonomy”. EC Bacteriology and Virology Research 2.1 (2016): 43-48.
Abstract
Three standards are applied for the naming of viruses, namely
a. The International Committee on Taxonomy of Viruses (ICTV)
b. The Baltimore classification of viruses
c. The microscopic introduction to virus taxonomy
It should be taken into account that viruses are often morphologically differentiated by shape, namely icosahedral, helical and complex shapes. Viruses can be named after the causative disease; after places where the disease was first reported; by means of the identified host; using scientific and documented evidence of the signs of disease and within the discovery of new and emerging viruses. An example can be illustrated by Rift Valley fever that is a viral zoonotic disease primarily affecting animal health but can also infect humans.
The ICTV was established historically in 1996 and this gave rise to an internationally agreed taxonomy for viruses. The unique name for each virus has now been sustained. Virus identification is recognised at the following levels, namely: order; family; sub-family; genus and species.
The Baltimore classification of viruses distinguishes major groups of viruses by their nucleic acid content that is DNA or RNA. All viruses need to produce positive-sense single-stranded RNA for the production of proteins.
The microscopic introduction to virus taxonomy ensured that viruses could be identified up to the genus classification level.
Selected virus examples include measles virus, rubella (German measles), chickenpox; Yellow fever virus, West Nile virus, Chikungunya virus and Rift Valley Fever virus.
In conclusion, viral classification systems are essential for retaining the specific naming of viruses and form the basis for additional discussion and further description. However, the concept of a virus is not a stable classification as viruses continue to evolve and is determined by technological advances and the contribution of scientific understanding.
Keywords: Virus taxonomy; Morphology; Cell tropism; Baltimore Classification; Virus nomenclature
Introduction
There are a number of reasons to understand the actual naming of viruses and three standards have been applied, namely:
a. The International Committee on Taxonomy of Viruses (ICTV)
b. The Baltimore classification of viruses and
c. The microscopic introduction to virus taxonomy [1,2].
Viruses are basically obligate intracellular parasites or entities and virus classification is a process of naming viruses and deliberately placing them into the taxonomic system [3]. Historically, viruses have been classified by phenotypic characteristics such as morphology, nucleic acid types, their modes of replication, the host organism and the types of diseases caused and recognised. Viruses are morphologically differentiated by shape, namely:
a. Icosahedral (examples include herpes simplex virus and poliovirus)
b. Helical (tobacco mosaic virus and rabies virus)and
c. Complex (bacteriophages and smallpox virus) [4].
There are various approaches to naming certain viruses and the following selected examples are included, namely:
a. Named after the disease
b. Named after the places where the actual disease was first reported
c. The identified host;
d. The scientific and documented evidence of the signs of disease and
e. The discovery of new and emerging viruses [5,6].
Viruses are composed of RNA or DNA single-stranded or double-stranded structures and can be further classified by whether they are undergoing reverse transcription (retroviruses), by whether they have a linear or circular genome and then finally according to the tissue that is affected [7].
The International Committee on the Taxonomy of Viruses (Ictv)
The ICTV was established in 1966 and was originally called the International Committee on the Nomenclature of Viruses (ICNV) [8]. This Committee was instructed to develop a universal taxonomic scheme to identify and address the nomenclature and classification of viruses [8]. These gave rise to an internationally agreed taxonomy for viruses, internationally agreed names for viral taxa that included species and sub-viral agents. This was communicated to the international community of virologists and an index of virus names was created [9]. The principles of ICTV was to maintain stability, to prevent any confusion and to sustain the unique identify of each name.
Virus identification is recognised at the following levels, namely:
a. order (virales);
b. family (viridae);
c. sub-family (virinae);
d. genus (virus) and
e. species.
An example of this ICTV classification would be the following, namely:
Order: Herpes virales
Family: Herpes viridae
Sub-family: Alphaherpes virinae;
Genus: Simplexvirus and
Species: Human herpesvirus1 and/or herpes simplex virus.
Baltimore Classification of Viruses
This was initially suggested by David Baltimore and viruses were divided into 7 Baltimore classes. This division was based on the genomic type, the mode of replication and the reality model of viral transcription [10,11]. Major groups of viruses are distinguished firstly by their nucleic acid content as either DNA (single-stranded DNA or double-stranded DNA) or RNA (single-stranded RNA or double-stranded RNA) [12]. Baltimore’s classification is based on the fact that all viruses need to produce positive-sense single-stranded RNA that produces proteins [12].
Microscopic Introduction to Virus Taxonomy
Microscopic classification of viruses came about from the routine usage of electron microscope and viral particles were viewed morphologically. Viruses could be identified up to the genus level [13,14]. Criteria need to be followed when viewing viruses under the transmission electron microscope and include the viral nucleocapsid that can be naked or enveloped and the size range in viral diameters. The nucleocapsid is composed of nucleic acids and capsomers and the viral envelope contains glycoprotein spikes, transmembrane proteins, lipoproteins and matrix proteins. These criteria could help to distinguish between different families without the use of the ICTV or Baltimore classifications [1]. Naked or non-enveloped virus families may have diverse size ranges and clinical virology examples include hepatitis E virus, Norwalk virus, rotavirus, adenovirus and papillomavirus.
Selected Virus Examples
Measles virus
The name measles virus comes from a Middle English word “Maselen” which means “many tiny spots” that characterises the rash [15]. The resulting infection is highly contagious and is transmitted through droplet spread. The clinical presentation is usually non-specific and can cause a rash, fever, dry cough, a sore throat and conjunctivitis. There is no therapeutic cure and only supportive treatment is considered [16].
German measles or rubella
This was called German measles as a German physician wrote a clear clinical description of its presentation in 1760 [17]. It is responsible for the clinical congenital rubella syndrome but the usual clinical presentation in older children and adults is mild, when compared to measles. It is managed through an effective vaccination programme called the MMR (measles, mumps and rubella) vaccine [18].
Chickenpox
This is one of two diseases caused by human herpes virus 3 (HHV-3) or more popularly the varicella-zoster virus (VZV). VZV is also known to cause another clinical entity called shingles. Chickenpox is a mild symptomatic disease usually affecting young children but can have severe complications in infants, adults and immunocompromised patients [18,19]. The disease is airborne and highly contagious [20]. The virus remains dormant in the dorsal root ganglia of all persons who have had chickenpox and can be reactivated later in life.
Yellow fever virus
Yellow fever virus was discovered in Cuba and it appears the name was derived from the skin pigmentation caused by jaundice [21]. It was hence discovered that yellow fever as a clinical entity was transmitted to humans from the bite of a mosquito [21]. This virus is endemic in Africa and Latin America. The disease presents with fever and jaundice leading to liver, kidney and cardiac disorders [22]. There is no treatment for this disease and supportive care remains critical. Vaccinations are essential for travellers to viral endemic areas and a vaccination booster every 10 years is highly recommended.
West Nile virus
This emerging viral infectious disease was first discovered in Uganda in 1937 and belongs to the Japanese encephalitis viral antigenic complex [23]. It is transmitted to humans through the bites of infected Culexsp mosquitoes that also feed on birds. This virus can cause fatal neurological disease in humans as no specific treatment or vaccine is currently available.
Chikungunya virus
The name for this virus is derived from the Makonde (the Makonde Plateau that is a border between the countries Mozambique and Tanzania) and means “that which bends up” and this refers to the posture gained as a result of painful arthritis. The name also means “the illness of the bended walker”. The disease originated in Central Africa and re-emergences have been recorded in Asia and Europe [24]. The clinical disease presents with fever, rash, headache, arthralgias and potential bleeding. There is no available vaccine and treatment is supportive [25].
Rift Valley fever
This is a viral zoonotic disease primarily affecting animals but can also infect humans [26]. Although it was first identified in 1931 during an investigation into an epidemic amongst sheep on a farm in the Rift Valley of Kenya, outbreaks were reported in Saudi Arabia, North Africa and sub-Saharan Africa. The majority of human infections arise from direct or indirect contact with blood or organs of infected animals. Clinical symptoms include fever, muscular and joint pains, headache and possible encephalitis [27].
S.No Virus
1 measles virus
2 German measles
3 Chickenpox
4 Yellow fever virus
5 West Nile virus
6 Chikungunya virus
7 Rift Valley fever virus
Table 1: Virus Taxonomy - Selected Virus Examples and Viral Diseases.
S.No Baltimore Classification of Viruses
1 Genomic type of the virus
2 The mode of replication
3 The different viral transcription models
4 The viral nucleic acid content (DNA or RNA)
5 Single-stranded DNA viruses
6 Double-stranded DNA viruses
7 Single-stranded RNA viruses
8 Double-stranded RNA viruses
9 Positive-sense single-stranded RNA viruses
10 Viral protein production
Table 2: The Baltimore Classification of Viruses.
Conclusion
The ICTV and Baltimore classifications for viral taxonomy are essential for the specific naming of viruses and can form the basis for further discussion or description. Viruses and the pathology, epidemiology, modes of transmission, clinical immunology and treatment of infectious diseases can now be studied with a precise understanding of the agent, as illustrated by the examples of the 1918 influenza pandemic and the eradication of the smallpox virus. The first images of a virus revealed their morphological complexity through a variety of shapes and this has lead to their ever-changing concepts. More recently, modes of viral replication, such as nuclear or cytoplasmic strategies and negative or positive DNA/RNA strand coding are being studied and recognised. Viruses are recognised anew through their own properties, relationships and capacities that adequately reflect the science of the time.
The concept of a virus is not a stable classification as viruses continue to evolve and this is determined by technological advances more so than scientific understanding.
Bibliography
  1. Mahy BM. “Emerging virus infections”. In Principles and Practice of Clinical Virology 6 (2009): 69-79.
  2. Holmes EC. “On the origin and evolution of the human immunodeficiency virus (HIV)”. Biological reviews of the Cambridge Philosophical Society 76.2 (2001): 239-254.
  3. Birkhead M and Paweska J. “A microscopic introduction to virus taxonomy”. Communicable Diseases Surveillance Bulletin 13.2 (2015): 52-61.
  4. Mahy BM. “The global threat of emerging infectious diseases”. Fighting Infection 21 (2000): 1-16.
  5. Halpin K., et al. “Emerging viruses: coming on a wrinkled wing and a prayer”. Clinical Infectious Diseases 44.5 (2007): 711-717.
  6. Worobey M. “Extensive homologous recombination among widely divergent TT viruses”. Journal of Virology 74.16 (2000): 7666-7770.
  7. Shors T. “Virus Architecture and Nomenclature”. Understanding Viruses 2 (2009): 70-85.
  8. Mushawar IK. “Recently discovered blood-borne viruses: are they hepatitis viruses or merely endosymbionts?”. Journal of Medical Virology 62.4 (2000): 399-404.
  9. World Bank. Investing in Health: World Development Report. Oxford UniversityPress (1993).
  10. Mackay IM. “Real-time PCR in the microbiology laboratory”. Clinical Microbiologyand Infection 10.3 (2004): 190-212.
  11. Mackay IM., et al. “Real-time PCR in virology”. Nucleic Acids Research 30.6 (2002): 1292-1305.
  12. Lin R and Liu Q. “Diagnosis and treatment of viral diseases in recipients of allogeneic hematopoetic stem cell transplantation”. Journal of Haematology and Oncology 6.94 (2013): 1-14.
  13. Carman B. “Molecular techniques should now replace cell culture in diagnostic virology laboratories”. Reviews in Medical Virology 11.6 (2001): 347-349.
  14. Boekh M., et al. “Factors influencing detection of quantitative cytomegalovirus antigenemia”. Journal of Clinical Microbiology 32.3 (1994): 832-834.
  15. Zuniga A., et al. “Attentuated measles virus as a vaccine vector”. Vaccine 25.16 (2007): 2974-2883.
  16. Clements CJ and Cutts FT “The epidemiology of measles: thirty years of vaccination”. Current Topics in Microbiology and Immunology 191 (1995): 13-33.
  17. Adamo MP., et al. “Analysis of gene expression in fetal and adult cells infected with rubella virus”. Virology 370.1 (2008): 1-11.
  18. Banatvala JE and Brown DWG. “Rubella”. The Lancet 363.9415 (2004): 1127-1137.
  19. Steiner I., et al. “The neurotropic herpes viruses: herpes simplex and varicella-zoster”. The Lancet Reviews 6.11 (2007): 1015-1028.
  20. Lehmann HC and Hartung H. “Varicella-zoster virus: another trigger of Guillain-Barre Syndrome?”. Clinical Infectious Diseases 51.5 (2010): 531-533.
  21. Barrett AD and Higgs S. “Yellow fever: a disease that has yet to be conquered” Annual review of entomology 52 (2007): 202-229.
  22. Jennings AD., et al. “Analysis of a yellow fever virus isolated from a fatal case of vaccine-associated human encephalitis”. Journal of Infectious Diseases 169.3 (1994): 512-518.
  23. Jupp PG. “The ecology of West Nile virus in South Africa and the occurrence of outbreaks in humans”. Annals of the New York Academy of Sciences 951 (2001): 143-152.
  24. Burt FJ., et al. “Phylogenetic relationships of southern African West Nile virus isolates”. Emerging Infectious Diseases 8.8 (2002): 820-826.
  25. Brighton SW and Simpson IW. “A destructive arthrophy following Chikungunya virus arthritis – a possible association”. Clinical Rheumatology 3.2 (1984): 253-258.
  26. Hazmi AL., et al. “Epidemic Rift Valley fever in Saudi Arabia: a clinical study of severe illness in humans”. Clinical Infectious Diseases 36.3 (2003): 245-252.
  27. Arishi HM., et al. “Vertical transmission of fatal Rift Valley fever in a newborn”. Annals of Tropical Paediatrics 26.3 (2006): 251-253.
Copyright: © 2016 Lynne M Webber. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PubMed Indexed Article

EC Pharmacology and Toxicology
LC-UV-MS and MS/MS Characterize Glutathione Reactivity with Different Isomers (2,2' and 2,4' vs. 4,4') of Methylene Diphenyl-Diisocyanate.

PMID: 31143884 [PubMed]

PMCID: PMC6536005


EC Pharmacology and Toxicology
Alzheimer's Pathogenesis, Metal-Mediated Redox Stress, and Potential Nanotheranostics.

PMID: 31565701 [PubMed]

PMCID: PMC6764777


EC Neurology
Differences in Rate of Cognitive Decline and Caregiver Burden between Alzheimer's Disease and Vascular Dementia: a Retrospective Study.

PMID: 27747317 [PubMed]

PMCID: PMC5065347


EC Pharmacology and Toxicology
Will Blockchain Technology Transform Healthcare and Biomedical Sciences?

PMID: 31460519 [PubMed]

PMCID: PMC6711478


EC Pharmacology and Toxicology
Is it a Prime Time for AI-powered Virtual Drug Screening?

PMID: 30215059 [PubMed]

PMCID: PMC6133253


EC Psychology and Psychiatry
Analysis of Evidence for the Combination of Pro-dopamine Regulator (KB220PAM) and Naltrexone to Prevent Opioid Use Disorder Relapse.

PMID: 30417173 [PubMed]

PMCID: PMC6226033


EC Anaesthesia
Arrest Under Anesthesia - What was the Culprit? A Case Report.

PMID: 30264037 [PubMed]

PMCID: PMC6155992


EC Orthopaedics
Distraction Implantation. A New Technique in Total Joint Arthroplasty and Direct Skeletal Attachment.

PMID: 30198026 [PubMed]

PMCID: PMC6124505


EC Pulmonology and Respiratory Medicine
Prevalence and factors associated with self-reported chronic obstructive pulmonary disease among adults aged 40-79: the National Health and Nutrition Examination Survey (NHANES) 2007-2012.

PMID: 30294723 [PubMed]

PMCID: PMC6169793


EC Dental Science
Important Dental Fiber-Reinforced Composite Molding Compound Breakthroughs

PMID: 29285526 [PubMed]

PMCID: PMC5743211


EC Microbiology
Prevalence of Intestinal Parasites Among HIV Infected and HIV Uninfected Patients Treated at the 1o De Maio Health Centre in Maputo, Mozambique

PMID: 29911204 [PubMed]

PMCID: PMC5999047


EC Microbiology
Macrophages and the Viral Dissemination Super Highway

PMID: 26949751 [PubMed]

PMCID: PMC4774560


EC Microbiology
The Microbiome, Antibiotics, and Health of the Pediatric Population.

PMID: 27390782 [PubMed]

PMCID: PMC4933318


EC Microbiology
Reactive Oxygen Species in HIV Infection

PMID: 28580453 [PubMed]

PMCID: PMC5450819


EC Microbiology
A Review of the CD4 T Cell Contribution to Lung Infection, Inflammation and Repair with a Focus on Wheeze and Asthma in the Pediatric Population

PMID: 26280024 [PubMed]

PMCID: PMC4533840


EC Neurology
Identifying Key Symptoms Differentiating Myalgic Encephalomyelitis and Chronic Fatigue Syndrome from Multiple Sclerosis

PMID: 28066845 [PubMed]

PMCID: PMC5214344


EC Pharmacology and Toxicology
Paradigm Shift is the Normal State of Pharmacology

PMID: 28936490 [PubMed]

PMCID: PMC5604476


EC Neurology
Examining those Meeting IOM Criteria Versus IOM Plus Fibromyalgia

PMID: 28713879 [PubMed]

PMCID: PMC5510658


EC Neurology
Unilateral Frontosphenoid Craniosynostosis: Case Report and a Review of the Literature

PMID: 28133641 [PubMed]

PMCID: PMC5267489


EC Ophthalmology
OCT-Angiography for Non-Invasive Monitoring of Neuronal and Vascular Structure in Mouse Retina: Implication for Characterization of Retinal Neurovascular Coupling

PMID: 29333536 [PubMed]

PMCID: PMC5766278


EC Neurology
Longer Duration of Downslope Treadmill Walking Induces Depression of H-Reflexes Measured during Standing and Walking.

PMID: 31032493 [PubMed]

PMCID: PMC6483108


EC Microbiology
Onchocerciasis in Mozambique: An Unknown Condition for Health Professionals.

PMID: 30957099 [PubMed]

PMCID: PMC6448571


EC Nutrition
Food Insecurity among Households with and without Podoconiosis in East and West Gojjam, Ethiopia.

PMID: 30101228 [PubMed]

PMCID: PMC6086333


EC Ophthalmology
REVIEW. +2 to +3 D. Reading Glasses to Prevent Myopia.

PMID: 31080964 [PubMed]

PMCID: PMC6508883


EC Gynaecology
Biomechanical Mapping of the Female Pelvic Floor: Uterine Prolapse Versus Normal Conditions.

PMID: 31093608 [PubMed]

PMCID: PMC6513001


EC Dental Science
Fiber-Reinforced Composites: A Breakthrough in Practical Clinical Applications with Advanced Wear Resistance for Dental Materials.

PMID: 31552397 [PubMed]

PMCID: PMC6758937


EC Microbiology
Neurocysticercosis in Child Bearing Women: An Overlooked Condition in Mozambique and a Potentially Missed Diagnosis in Women Presenting with Eclampsia.

PMID: 31681909 [PubMed]

PMCID: PMC6824723


EC Microbiology
Molecular Detection of Leptospira spp. in Rodents Trapped in the Mozambique Island City, Nampula Province, Mozambique.

PMID: 31681910 [PubMed]

PMCID: PMC6824726


EC Neurology
Endoplasmic Reticulum-Mitochondrial Cross-Talk in Neurodegenerative and Eye Diseases.

PMID: 31528859 [PubMed]

PMCID: PMC6746603


EC Psychology and Psychiatry
Can Chronic Consumption of Caffeine by Increasing D2/D3 Receptors Offer Benefit to Carriers of the DRD2 A1 Allele in Cocaine Abuse?

PMID: 31276119 [PubMed]

PMCID: PMC6604646


EC Anaesthesia
Real Time Locating Systems and sustainability of Perioperative Efficiency of Anesthesiologists.

PMID: 31406965 [PubMed]

PMCID: PMC6690616


EC Pharmacology and Toxicology
A Pilot STEM Curriculum Designed to Teach High School Students Concepts in Biochemical Engineering and Pharmacology.

PMID: 31517314 [PubMed]

PMCID: PMC6741290


EC Pharmacology and Toxicology
Toxic Mechanisms Underlying Motor Activity Changes Induced by a Mixture of Lead, Arsenic and Manganese.

PMID: 31633124 [PubMed]

PMCID: PMC6800226


EC Neurology
Research Volunteers' Attitudes Toward Chronic Fatigue Syndrome and Myalgic Encephalomyelitis.

PMID: 29662969 [PubMed]

PMCID: PMC5898812


EC Pharmacology and Toxicology
Hyperbaric Oxygen Therapy for Alzheimer's Disease.

PMID: 30215058 [PubMed]

PMCID: PMC6133268


News and Events

June Issue Release

We always feel pleasure to share our updates with you all. Here, notifying you that we have successfully released the June issue of respective journals and the latest articles can be viewed on the current issue pages.

Submission Deadline for Upcoming Issue

ECronicon delightfully welcomes all the authors around the globe for effective collaboration with an article submission for the upcoming issue of respective journals. Submissions are accepted on/before July 05, 2022.

Certificate of Publication

ECronicon honors with a "Publication Certificate" to the corresponding author by including the names of co-authors as a token of appreciation for publishing the work with our respective journals.

Best Article of the Issue

Editors of respective journals will always be very much interested in electing one Best Article after each issue release. The authors of the selected article will be honored with a "Best Article of the Issue" certificate.

Certifying for Review

ECronicon certifies the Editors for their first review done towards the assigned article of the respective journals.

Latest Articles

The latest articles will be updated immediately on the articles in press page of the respective journals.