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Clinical Neurovirology
Clinical Neurovirology
Second Edition
Edited by
Avindra Nath
Joseph R. Berger
Second edition published 2020
by CRC Press
6000 Broken Sound Parkway NW, Suite 300, Boca Raton, FL 33487-2742
This book contains information obtained from authentic and highly regarded sources. While all reasonable efforts have been made to publish reliable data and
information, neither the author[s] nor the publisher can accept any legal responsibility or liability for any errors or omissions that may be made. The publishers wish
to make clear that any views or opinions expressed in this book by individual editors, authors or contributors are personal to them and do not necessarily reflect
the views/opinions of the publishers. The information or guidance contained in this book is intended for use by medical, scientific or health-care professionals and
is provided strictly as a supplement to the medical or other professional’s own judgement, their knowledge of the patient’s medical history, relevant manufacturer’s
instructions and the appropriate best practice guidelines. Because of the rapid advances in medical science, any information or advice on dosages, procedures or
diagnoses should be independently verified. The reader is strongly urged to consult the relevant national drug formulary and the drug companies’ and device or
material manufacturers’ printed instructions, and their websites, before administering or utilizing any of the drugs, devices or materials mentioned in this book.
This book does not indicate whether a particular treatment is appropriate or suitable for a particular individual. Ultimately it is the sole responsibility of the medi-
cal professional to make his or her own professional judgements, so as to advise and treat patients appropriately. The authors and publishers have also attempted
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intent to infringe.
ISBN: 9781498733168 (hbk)
ISBN: 9781315113913 (ebk)
Typeset in Minion
by Lumina Datamatics Limited
To my wife, Sandy, and children, Aaron, Michael, and Rachel, whose accomplish-
ments have been a source of great pride
Joseph R. Berger
To my wife, Nancy, and children, Nalanie and Samir, and their spouses, Stephen and Kathleen,
for their infectious personalities and who are also my pride and joy
Avindra Nath
Contents
Preface ix
Acknowledgments xi
Editors xiii
Contributors xv
vii
viii Contents
Index 443
Preface
Humanity has but three great enemies; Fever, famine and war; of these by far the greatest, by far the most terrible, is fever.
ix
Acknowledgments
We would like to acknowledge our mentors, colleagues, trainees, and patients who have been the source of knowledge
and inspiration.
xi
Editors
Dr. Avindra Nath, MD, is the Chief of the Section of Dr. Joseph R. Berger, MD, is Professor of Neurology
Infections of the Nervous System at the National Institute and Associate Chief of the Multiple Sclerosis Division of
of Neurological Disorders and Stroke. He was previously the Department of Neurology at the Perelman School of
Professor in the Department of Neurology and Director of the Medicine at the University of Pennsylvania in Philadelphia.
Division of Neuroimmunology and Neurological Infections His career has been dedicated to the diagnosis, treatment,
at Johns Hopkins University. His career has been dedicated and investigation of neuroinfectious and neuroinflam-
to studying the clinical manifestations, pathophysiology, and matory disorders. His foray into neuroinfectious diseases
developing treatments for brain infections since the begin- started with the investigation of the neurological compli-
ning of the AIDS pandemic. He has traveled to several coun- cations of HIV/AIDS while at the University of Miami at
tries to study these infections, including Liberia during the the inception of the AIDS pandemic and an endowment
Ebola epidemic. He teaches medical students, residents, and there established the Whigham-Berger Endowed Chair, the
clinical fellows on CNS infections, for which he has received first endowed chair for the study of the neurological com-
several teaching awards. He frequently talks at grand rounds, plications of HIV/AIDS. Dr. Berger continued his research
seminars, and conferences around the world on viral infec- in HIV and progressive multifocal leukoencephalopathy
tions of the brain and has been teaching courses on viral (PML) while at the University of Kentucky, where he was
encephalitis at the American Academy of Neurology for over Chairman of the Department of Neurology from 1995 to
20 years. His laboratory research is focused mainly on retro- 2013. With Dr. Robert Levy, he co-founded and co-chaired
viral infections, particularly HIV infection. More recently, the international Neuroscience of HIV conference. He is
his laboratory is studying the pathophysiology of Ebola and a fellow of the American College of Physicians, American
Zika viruses. He is the past President of the International Academy of Neurology, and the American Neurological
Society of Neurovirology (ISNV) and an elected member of Association. Among his many awards are the Pioneer
the Association of American Physicians. He is the recipient Award from the International Society of Neurovirology
of the Pioneer Award from the ISNV and the Wybran Award and the Distinguished Teaching Award from the American
from the Society of Neuroimmune Pharmacology. Neurological Association.
xiii
Contributors
xv
xvi Contributors
Introduction: Epidemiology,
socioeconomic impact, and
challenges ahead
1.1 VIRUS STRUCTURE serially passaged from one host to another, whereas viruses
undergo multiplication. Although humans have been aware
1.1.1 General nature of viruses of viruses for a relatively short period of time, these agents
are probably as old as life itself and have probably coevolved
Although the concept of an infectious “virus” is only about with other forms of life.
100 years old, diseases caused by these agents have been Viruses are among the simplest and smallest of currently
known since ancient times. For example, both rabies and known living organisms. In fact, because of their simplic-
polio, which are discussed in greater detail in later chapters ity, there is some debate as to whether viruses should be
of this volume, appear to have been known in Egypt around considered living. Most viruses consist of both protein and
2000 bc, almost 1000 years before the time of the Pharaoh nucleic acid. Viroids (plant pathogens that consist solely of
Tutankhamen. Significant work preceding and during the RNA) and prions (agents that appear to consist solely of pro-
nineteenth century ce allowed visualization of bacteria tein) are exceptions. Viruses generally exist in two forms.
and established their disease-causing properties. It became The actively replicating virus inside an infected cell is the
appreciated toward the end of the nineteenth century that form that may be considered “alive.” The extracellular form
some agents capable of causing illness were small enough to of the virus is known as the virion. The virion is analogous
pass through filters known to block bacteria. Thus, the term to a seed or spore. It generally is a stable “crystalline” struc-
virus (Latin for poison) was coined to describe these “fil- ture whose primary function is to protect the genetic mate-
terable toxins.” However, it was soon realized that viruses rial until the nucleic acid reaches the interior of a suitable
were different from poisons. Toxins can be diluted when host cell. No virus is capable of growing by itself. All must
3
4 Introduction to virus structure, classification, replication, and hosts
make use of macromolecular “building blocks” (amino (e.g., vaccinia virus and the smallpox agent Variola major)
acids, nucleotides, and, in some cases, lipids) and employ are members of the Poxviridae family. Poxvirus virions are
enzymes found within living cells. Thus, all viruses are obli- generally approximately 200 × 300 nm in size (Figure 1.1) and
gate intracellular parasites. are barely visible by light microscopy. Ebolaviruses, the caus-
ative agents of lethal Ebola hemorrhagic fever, and members
1.1.2 Virus morphology of the Filoviridae family are filamentous virions with diam-
eters of only 80 nm but lengths of up to 14,000 nm [1]. As
1.1.2.1 VIRION SIZE AND COMPLEXITY another example, several viruses colloquially known as giant
There is enormous variability in the size of virions. The small- viruses can infect amoebas. These include Mimiviruses,
est animal virions are the parvoviruses (e.g., the human Pandoraviruses, Megaviruses, and Pithoviruses whose
parvovirus B19), which belong to the family Parvoviridae. virions can reach up to 1.5 μm [2]. There also is significant
As detailed later in Section 1.5, almost all viruses are orga- variability in virion complexity. Parvoviruses consist of
nized into families, which are designated with an italicized a small piece of nucleic acid surrounded by 60 copies of a
name ending with the suffix-viridae. Groups of viruses single protein. Other viruses, such as the Polyomaviridae
(families) may be referred to by their italicized family and the Papillomaviridae, may be more complex and larger,
name (e.g., Parvoviridae) or may be referred to by a nonita- composed of a larger piece of nucleic acid and more than
licized generic name (e.g., parvoviruses). Both conventions 60 copies of a single protein. Most virions are even more
are used in this chapter. Parvovirus virions are less than complicated and larger. Some (e.g., adenoviruses) contain a
20 nm in diameter (Figure 1.1). The largest animal viruses single piece of nucleic acid surrounded by multiple different
proteins that are not present in the same quantities; some
(e.g., rubella virus and various equine encephalitis viruses,
DNA RNA
which belong to the family Togaviridae) contain the same
number of various proteins but also contain a lipid mem-
ssDNA ssRNA
Parvoviridae Picornaviridae
brane (envelope); some (e.g., rabies virus, which belongs to
the family Rhabdoviridae; measles virus and mumps virus,
Non-Enveloped
(−) ssRNA necrotic stunt virus of the Nanoviridae family have a seg-
mented genome encapsidated in individual capsids. These
Herpesviridae Paramyxoviridae multipartite viruses require all the sub-particles to infect a
cell in order to provide all components for replication [3].
if provided by the host cell, are located within the host’s 9–12 segments (depending upon the specific genus of virus)
nucleus, so most DNA viruses replicate inside the host of double-stranded RNA, all of which must be present in a
nucleus. One group of viruses that are exceptions to this virion for it to be infectious. The segmented nature of these
generalization are the Poxviridae, large complex viruses that types of viral genomes has dramatic ramifications with
encode all their necessary DNA enzymes and thus can rep- regard to their pathogenesis (reviewed in Refs. [6,7]).
licate in the cell’s cytoplasm. Conversely, RNA viruses do
not generally require DNA enzymes (although retroviruses 1.1.2.3 VIRAL PROTEINS
are an exception), so RNA viruses generally replicate in the Viral proteins can be generally classified as either struc-
cell’s cytoplasm. In addition to the retroviruses, which use tural or nonstructural. By convention, structural proteins
a DNA intermediate, some RNA viruses, such as the influ- are those that are present within a virion particle. Their
enza viruses, carry out some of their replicative steps in the identities are usually determined by examining the protein
cell’s nucleus because they need to “steal” components from content of highly purified preparations of viral particles.
cells before those cellular elements leave the nucleus. For any given virus there is usually a fixed and characteris-
The viral nucleic acid, whether DNA or RNA, may be tic number of proteins located within the virion. For exam-
either single-stranded (ss) or double-stranded (ds). If single- ple, poliovirus virions contain a single copy of one protein
stranded, the genome may be of either positive (+) or nega- (called VPg) (VP usually indicates virion protein) and 60
tive (−) polarity. By convention, messenger RNA (mRNA), copies each of four other proteins (called VP1, VP2, VP3,
which is “read” by ribosomes to translate the mRNA into and VP4). By contrast, nonstructural proteins are those
protein, is considered (+) polarity. Thus, the template that are encoded by the virus and are found in infected cells
DNA or RNA strand that is transcribed to produce the but not within the purified virion. Nonstructural proteins
mRNA is considered (−) polarity. The important ramifica- are generally enzymatic. They carry out specific enzymatic
tions of these differences in viral nucleic acid and polarity functions within the cell but are not included within the
with regard to classification and replication are described viral particle. However, some structural proteins also may be
more fully in later sections of this chapter. enzymes. Within the virion the viral nucleic acid, whether
The viral genome may range in size and configuration. RNA or DNA, is usually surrounded by a protective pro-
The term genome refers to all the nucleic acid of a virus, tein coat built from structural proteins. Because the genetic
whereas gene usually refers to the part of the nucleic acid code is such that nucleotide base triplets encode each amino
genome that encodes a specific viral protein. The smallest acid, it is not possible for any genetic material to encode a
viruses (e.g., parvoviruses) have genomes of approximately single protein sufficiently large to protect the genome that
5000 nucleotides (=5 kilobases, or 5 kb) that contain two encodes it. Thus, for genetic efficiency the protective protein
genes. The largest human viruses (e.g., poxviruses and coat is usually constructed from multiple copies of one or a
herpesviruses) can have genomes larger than 200 kilo- few proteins.
base pairs (200 kbp; “pairs” because their nucleic acid is
double-stranded) and can therefore potentially encode 1.1.2.4 HOST PROTEINS
more than 250 proteins. Pandoraviruses, a member of the Some virions also contain host proteins. Among the best
amoeba-infecting “giant virus” group, have a genome of known are the human immunodeficiency virus-1 (HIV-1)
approximately 1.9–2.5 million bp which could potentially (e.g., [8,9]). Other studies suggest that viruses such as her-
encode over 2500 proteins [4]. Most viruses have genomes pesviruses [10], filoviruses [11], and influenza viruses [12]
whose sizes fall between these extremes. For most families may also incorporate functional host-derived proteins.
of viruses, all viral genes are located on a single contigu- These may play a role in the virus lifecycle and protect viri-
ous linear piece of nucleic acid, with the same gene gener- ons from, for example, complement-mediated lysis [13,14].
ally located in the same position on the genome in every Many such observations point toward a biologically relevant
virion within that family. A few viruses (e.g., hepatitis B role for incorporated host proteins in viruses, yet further
virus, a member of the Hepadnaviridae, which, because it is research and refinement in virion preparation and purifica-
not known to be neurotropic, is not covered in this volume tion would be useful to exclude the possibility of contami-
and the Polyomaviridae, which includes the neurotropic nation during sample preparation.
JC virus) have a circular rather than linear genome. Some
viruses have segmented genomes. For example, the human 1.1.3 Capsid morphology
influenza virus genome consists of eight separate segments
of RNA that encode at least 15 different proteins. To opti- Collectively, the nucleic acid and the protein that is closely
mize genome size, five of the eight RNA segments encode associated to protect it form a nucleoprotein complex
more than one protein due to alternative splicing or initia- known as the viral capsid. There are two general ways in
tion or ribosomal frameshift. To be infectious, a virion must which repeating units of proteins can be organized so that
contain at least one copy of each of the eight gene segments, they effectively protect the nucleic acid. One method is to
although recent research has highlighted the possibility wrap the protein along the nucleic acid, allowing each pro-
that influenza viruses may behave similarly to multipar- tein building block to interact with part of the nucleic acid.
tite viruses [5]. Likewise, the Reoviridae genome consists of This results in a helical arrangement. Examples of this type
6 Introduction to virus structure, classification, replication, and hosts
of arrangement include tobacco mosaic virus (Figure 1.1), 1.1.4 Other virion components
an extensively studied plant virus. In addition, most cur-
rently known (−) sense animal RNA viruses (e.g., the In some cases, the viral capsid structure is surrounded by
Orthomyxoviridae, Paramyxoviridae, and Rhabdoviridae) a lipid membrane (envelope). Thus, presence or absence of
encase their RNA in a helical configuration. The second an envelope is another convenient way to organize viruses
general method to protectively surround the nucleic acid is into groups (Figure 1.1). When an envelope is present, the
to build a three-dimensional cage. The most efficient way to nucleoprotein structure is then referred to as a nucleocapsid.
build a three-dimensional cage that has no holes in it from Some viruses, such as the Orthomyxoviridae (e.g., influenza
the smallest number of types of building blocks is to join virus), the Paramyxoviridae (e.g., measles virus), and the
20 equilateral triangles to form an icosahedron. The icosa- Rhabdoviridae (e.g., rabies virus) contain helical nucleocap-
hedron is a nearly spherical object, possessing 12 corners sids surrounded by a membrane. In addition, icosahedral
(vertices), 20 triangular faces, and 30 edges. Examples of nucleocapsids may be surrounded by an envelope, as seen
this type of arrangement include poliovirus and JC virus with the Flaviviridae (e.g., dengue virus), Togaviridae (e.g.,
(Figure 1.1). A few viruses wrap their nucleic acid in a pro- rubella virus) and Herpesviridae (e.g., herpes simplex viruses).
tective coat that is neither helical nor icosahedral. For exam- In contrast to viral proteins and nucleic acid sequence, both
ple, retrovirus capsids are conical and poxvirus capsids are of which are specified within the viral genetic code, the lip-
ovoid (Figure 1.1). ids within the membrane are provided exclusively by the
The size of helical capsids is determined by the length of host cell. For most enveloped viruses, lipid membranes are
nucleic acid. The size of icosahedral capsids is determined normally acquired as the nucleocapsid passes through a cel-
by the size of each protein and by the number of proteins lular membrane, whereas a few viruses assemble their enve-
that generate the cage. To increase the number of proteins lopes de novo within the cell (discussed in greater detail in
that participate in building the cage, without introducing Section 1.6).
holes in the cage, there are only certain sets of protein num-
bers that can be used. This geometric problem was solved by 1.2 VIRUS CLASSIFICATION
Caspar and Klug [15], who introduced the concept of trian-
gulation numbers (T values) to describe icosahedral com- 1.2.1 Classification schemes
plexity. The simplest icosahedron is built from 60 identical
protein subunits (a pentameric aggregate at each of the 12 There are currently more than 3600 known virus species
vertices; 5 × 12 = 60) and is described as having a triangula- organized into approximately 56 families [20]. It is highly
tion value of 1 (T = 1). Parvoviruses are examples of such probable that this list will increase in the future because
an arrangement. To build larger icosahedral capsids, addi- there is the potential to discover additional viruses. In order
tional proteins have to be added, either on each of the 20 to simplify research on, and discussion of, these viruses, it
faces, or on each of the 30 edges, or on some combination of is essential to classify them in a manner that highlights their
faces and edges. Other proteins are usually added as hexa- similarities and differences. Several classification schemes
meric arrays (although adenoviruses and polyomaviruses have been developed to accomplish this task.
are notable exceptions). Thus, the next-most complicated
icosahedron would be one in which hexameric arrays were 1.2.1.1 THE FORMAL CLASSIFICATION SCHEME
added in the middle of each icosahedral face. The resulting Most organisms are classified according to the kingdom, phy-
structure would have (5 × 12) + (6 × 20), or 180, proteins lum, class, order, family, genus, and species. Most viruses, on
and is referred to as a T = 3 icosahedron. Strictly speaking, the other hand, are formally classified into families, subfam-
a T = 2 structure would have holes in it and so far no T = 2 ilies, genera and species, based on the similarities and dif-
structure has been identified. In general, the total number ferences between them. For example, members of the family
of proteins that form the icosahedral capsid is the triangu- Retroviridae all contain two copies of a (+)sRNA genome
lation number × 60. Notable exceptions to this general rule that is replicated via a dsDNA intermediate. No other family
include adenoviruses, polyomaviruses and some reoviruses. contains viruses with this characteristic. The Herpesviridae
Adenoviruses add trimeric arrays instead of hexameric family also is unique, because it contains viruses with lin-
arrays on icosahedral faces and edges [16], and polyoma- ear dsDNA genomes surrounded by an icosahedral cap-
viruses are built exclusively from pentameric arrays [17]. sid, an envelope with glycoprotein spikes, and a tegument
Reoviruses are composed of multilayered capsids. Some (a space between the capsid and the envelope that contains
reoviruses that possess prominent turrets on their inner- proteinaceous material). The formal classification of viruses
most capsids can omit protein capsid arrays near their verti- is overseen by the International Committee on Taxonomy
ces in the outer capsid because the turrets “block” the holes of Viruses (ICTV). In addition, based upon immunological
present in the outer capsid [18]. In addition, they appear to or molecular differences, viruses can sometimes be placed
violate the foregoing rules because their innermost capsids in lower levels of classification, which, depending upon the
contain 120 copies of major structural proteins. However, nomenclature for the specific group of viruses, can be known
rather than using the “forbidden” T = 2 organization, these as subspecies, strains, serotypes, clades, or variants. Except
viruses use a T = 1 organization of 60 dimers [19]. for the family names, which are italicized, capitalized, and
1.2 Virus classification 7
end in the suffix-viridae, there is no formal Latinized bino- scheme. In this scheme, viruses are placed in one of seven
mial nomenclature for viruses. Instead, a virus species is classes (Figure 1.2). Class I viruses harbor a dsDNA genome
usually known by a nonitalicized, nonunderlined, uncapi- that is used to transcribe mRNA, which is then translated into
talized common name, such as poliovirus. protein. Most of these viruses use host enzymes for the syn-
thesis of mRNA. Examples of such viruses that are discussed
1.2.1.2 THE EPIDEMIOLOGICAL AND ETIOLOGICAL in subsequent chapters of this volume are the Adenoviridae,
CLASSIFICATION SCHEMES Herpesviridae, and Polyomaviridae. Class II viruses have an
Viral classification schemes can also be based on epidemiol- ssDNA genome, which is usually negative sense in currently
ogy or etiology, with the possibility of a specific virus being known animal viruses and positive sense in non-animal
placed in several categories. Enteric viruses enter the body by viruses. The genome of (−)ssDNA viruses can be directly
ingestion and usually replicate primarily in the gastrointes- transcribed into mRNA. However, (+)ssDNA viruses must
tinal tract. Examples of such viruses are the Picornaviridae make a (−)ssDNA copy to act as a template for the syn-
(enterovirus genus), the Reoviridae, the Parvoviridae, and thesis of mRNA (e.g., parvovirus B19). Class III viruses
the Adenoviridae. Respiratory viruses are acquired by (e.g., Reoviridae) have dsRNA genomes, and mRNA is tran-
inhalation of aerosols or hand-to-face contact and usually scribed from the (−) sense strand. Class IV viral genomes are
replicate in the respiratory tract. This group includes the (+)ssRNA molecules. No transcription is required because
Picornaviridae (rhinovirus genus), the Paramyxoviridae, the genome can serve directly as mRNA. Class IV viruses
the Orthomyxoviridae, and the Adenoviridae. Arboviruses relevant to this volume are dengue virus, many enteroviruses
(arthropod-borne viruses) are transmitted by the bites of and rubella virus. The class V viral genome is (−)ssRNA,
insects or by inhalation of rodent droppings. Some common which serves as a template for the synthesis of mRNA. Rabies
arboviruses are found in the Alphatogaviridae, Flaviviridae, virus, measles virus, mumps virus and influenza virus belong
Rhabdoviridae, and Reoviridae families. Sexually transmit- to this class. Class VI, the last group, comprises retroviruses
ted viruses are transmitted through intimate contact that
generally involves the exchange of body fluids. They can I
cause local or general infections. Human immunodeficiency
dsDNA
virus is a well-known example of a sexually transmitted
VII Adenoviridae II
virus. Oncogenic viruses are often transmitted in much the Herpesviridae
dsDNA* - RT Papillomaviridae ssDNA
same manner as sexually transmitted viruses and replicate Polyomaviridae
V
genomic composition and virion morphology (Figure 1.1).
As indicated earlier, the viral genome can be DNA or RNA,
Figure 1.2 The Baltimore transcription scheme classifies
single-stranded or double-stranded, negative or positive
viruses based on their genomic nucleic acid content
sense in polarity, linear or circular, segmented or non- and on the strategies used to produce messenger
segmented. The presence or absence of a lipid envelope is RNA (mRNA). Virus genomes can be composed of RNA or
also important, and the overall shape of the capsid (heli- DNA that is either single-stranded (ss) or double-stranded
cal, icosahedral, or otherwise) and virion (spherical, bullet- (ds). For RNA viruses, the polarity of the ssRNA can be
shaped [e.g., Rhabdoviridae], or pleomorphic [lacking a either positive (+) or negative (−). By definition, mRNA is
defined shape] [e.g., the myxoviruses Orthomyxoviridae and positive stranded. Note that Class IV viruses have (+)
Paramyxoviridae]) also may be taken into consideration. RNA that can serve directly as mRNA as soon as the
viral genome enters the cell. Class VI and VII viruses
1.2.1.4 THE BALTIMORE CLASSIFICATION SCHEME can undergo reverse-transcription (RT) whereby RNA is
converted into DNA. In the case of Class VI retroviruses,
The mechanisms by which the viral genome is transcribed to this happens via a DNA/RNA hybrid to generate the
produce mRNA for protein production is the basis for another dsDNA intermediate. Intermediate steps toward
classification strategy. This classification was devised by mRNA synthesis are shown as green boxes. (Compiled
Dr. David Baltimore [21] and is known as the Baltimore from http://viralzone.expasy.org/all_by_species/254.html.)
8 Introduction to virus structure, classification, replication, and hosts
that contain (+)ssRNA genomes. The (+)ssRNA, unlike in Single-stranded DNA viruses that belong to class II have
the viruses of class IV, does not serve as mRNA. The pro- only a few members that infect humans. The human parvo-
duction of mRNA requires the synthesis of a dsDNA inter- virus B19 contains a (−)ssDNA genome encased in a nonen-
mediate, followed by transcription of the dsDNA. A new veloped icosahedral capsid. B19 is currently not associated
group, Class VII, contains the Hepadnaviridae, viruses with neuropathology and therefore is not covered in this
with a partial dsDNA genome that replicates through an volume.
RNA intermediate.
Although the Baltimore classification scheme is based 1.2.2.2 RNA VIRUSES
on the transcription strategies of viruses, the various Of all viruses, RNA viruses are responsible for causing
classes usually can be distinguished by the manner in the most diseases worldwide [22–24]. Like DNA viruses,
which the viral genomes are replicated. Class I viruses use the RNA viruses vary widely in genome sizes, gene orga-
their dsDNA genomes as a template to synthesize more nizations, genome structures, and virion structures.
dsDNA during genome replication. As in transcription, this The RNA viruses are more diverse than the DNA viruses,
replication is usually carried out by host enzymes. Class VII and there is the additional complication of segmented
Hepadnaviridae are an exception to this generalization; genomes in some human pathogens. Some of the nonenvel-
replication takes place through an RNA intermediate that oped dsRNA viruses are neuropathogenic in animals but are
is longer than the genome. Class II viruses go through a currently not believed to be neuropathogenic in humans.
replicative intermediate to copy their genomes. For exam- There are no known enveloped dsRNA viruses that infect
ple, (+)ssDNA viruses must make a (−)ssDNA copy to humans. The ssRNA virus group contains many neuro-
act as a template for more (+)ssDNA. In the case of pathogenic members. Relevant nonenveloped examples are
class III viruses, the mRNA that was used for protein the (+)ssRNA icosahedral enteroviruses. Enveloped exam-
synthesis is copied by viral enzymes into a (−) sense ples include (+)ssRNA viruses such as the spherical retrovi-
RNA that remains associated with the mRNA template ruses HIV and HTLV, rubella virus, as well as members of
to form the progeny dsRNA. Class IV viruses have (+) the Flaviviridae family such as dengue, Japanese encephali-
ssRNA genomes. A (−)ssRNA intermediate is produced, tis, West Nile and Zika viruses. Enveloped (−)ssRNA viruses
which then serves as the template for more (+)ssRNA. with neuropathogenic properties include the bullet-shaped
Class V viruses use the same replication strategy as class rabies virus and the pleomorphic measles virus, mumps
IV viruses, except that they start with a (−)ssRNA genome virus, and influenza virus, the last one of which has a seg-
and use a (+)ssRNA strand as an intermediate. In class mented genome.
VI, (+)ssRNA genomes are replicated by a unique mecha-
nism. The (+)ssRNA is used as a template to synthesize (−) 1.2.2.3 UNCLASSIFIED AGENTS
ssDNA, which in turn serves as a template for the synthe- Interestingly, the foregoing schemes are unsuccessful in
sis of a (+)ssDNA strand. The resulting dsDNA molecule classifying several infectious agents, namely viroids and
is transcribed into mRNA or used to synthesize progeny prions. As indicated earlier, viroids are composed solely of
(+)ssRNA genomes. nucleic acid and infect only plants. Prions are more medi-
cally relevant. They appear to consist solely of protein and
1.2.2 Integration of classification schemes are believed to be the causative agents of Creutzfeldt–Jakob
syndrome, kuru, and various subacute spongiform enceph-
1.2.2.1 DNA VIRUSES alopathies. Because these agents are so obviously unique in
Any number of classification schemes may be employed by their composition, they remain unclassified.
researchers and healthcare professionals, but for our pur- As described, many classification schemes are used today.
pose, it is simpler to separate viruses according to their Although the various classification strategies have been
genomes (whether the genome is DNA or RNA, ss or ds) useful for organizing the large numbers of known viruses,
and virion morphology (whether the virus has an enve- this chapter focuses on neuropathogenic human viruses.
lope and the overall shape of the particle). DNA viruses This theme is reflected in later chapters of this volume.
follow a more conventional replication strategy, although
their genome shapes, sizes, and organizations, as well as 1.3 VIRAL REPLICATION
the virion structures, are quite varied. Double-stranded
DNA viruses that belong to class I of the Baltimore clas- Viral replication is a complex process that is being heav-
sification scheme can be further divided based upon pres- ily investigated using both traditional virology as well as
ence or absence of an envelope. Relevant viruses that lack systems biology approaches. Modern techniques such as
an envelope include JC virus and adenovirus, both of RNA microarrays, next-generation sequencing and mass
which have icosahedral capsids. Examples of enveloped spectrometry-based proteomics have combined with
dsDNA viruses are members of the family Herpesviridae, advances in bioinformatics, led to a better understanding
including the herpes simplex viruses, varicella zoster virus, of virus–host interactions. Still, there is great diversity in
Epstein–Barr virus, cytomegalovirus, and human herpes- methods employed by different viruses, with adaptations
viruses. Herpesviruses have an icosahedral nucleocapsid. depending not only on the types of cells they can infect but
1.3 Viral replication 9
also on the specific replicative machinery each virus car- This is distinct from the eclipse period, which ends with
ries and the context of the host immunological response. the first detectable infectious virus that may be found
Furthermore, the current inability to culture some viruses intracellularly. The differences in assembly requirements of
in the laboratory contributes to lack of understanding of enveloped viruses, as contrasted to nonenveloped viruses,
their replication cycles. also lead to fundamental differences in whether intracel-
The replication of viruses can occur only within a living lular infectious virions are produced. An enveloped virus
cell because, as indicated earlier, they are obligate intracel- that matures by budding through the external membrane
lular parasites that are absolutely dependent on host cell does not exist as an infectious virus until it leaves the cell;
machinery for replication. Despite significant differences thus, there is no intracellular infectious virus (Figure 1.3b).
in the details of replication (as implied by the Baltimore The redetection and subsequent rapid rise of infectious
scheme), there are several common features. Two approaches virus, whether enveloped or nonenveloped, and intracellu-
can be used to describe the viral life cycle. The first approach lar or extracellular, denotes the end of the eclipse period and
employs a growth curve. The second is a more detailed the beginning of the productive or rise period. This period,
chronological description of viral life cycle events. initiated upon intracellular assembly of virions, is marked
by exponential rise in virus numbers and is characteristic
1.3.1 The viral growth curve of most viruses. The burst refers to the time point where
cell lysis occurs, which results in the subsequent release
A viral growth curve is calculated by measuring the amount and detection of cell-free virus.
of infectious virus present within and/or released from cells Several terms are used to describe the various types of
over a period of time. Typical growth curves are depicted viral infections that can occur in people. The more common
in Figure 1.3 for both a non-enveloped (Figure 1.3a) and type of infection that a virus can cause is an acute infec-
an enveloped (Figure 1.3b) virus. Details of a particu- tion, which is characterized by a rapid onset, visible symp-
lar growth curve (such as time between phases and total toms, and short duration (e.g., influenza virus). A chronic
virus released) will depend on the virus type and cell type. or persistent infection, unlike acute infections, which can
The infectious virus added to cells initially seems to dis- end in weeks, can last from years to indefinitely. In such
appear. This period, which corresponds to the virus being cases, the virus often reproduces at a much slower rate and
uncoated (see below), is termed the eclipse period and can can even result in an infected individual being apparently
range from 3 to 12 hours for animal viruses. During the symptom-free (e.g., herpesviruses and hepatitis B virus).
eclipse period, most of the infectious virus has entered the A latent virus infection refers to viruses that stop reproduc-
host cell and is undergoing replication as indicated by ing as they enter a state of dormancy, only to become active
the detection of new viral nucleic acid and proteins prior again at a later time point (e.g., herpesviruses). Like patients
to detection of progeny infectious virus. Another more with chronic infections, the patient with a latent virus infec-
general term often used is latent period, for the period that tion may not exhibit any symptoms until the virus becomes
begins with the onset of infection and ends with the first activated.
newly assembled detectable extracellular infectious virus.
100 100
Nucleic acid Nucleic acid
Cell-free
Viral nucleic acid
10 virus 10
PFU per cell
Cell-
1 associated 1
θ
virus
Cell-free
* *
virus
0.1 0.1
0 6 12 18 0 6 12 18
Attachment Hours Post-infection Attachment Hours Post-infection
and entry and entry
Rise period Rise period
Eclipse period Release Eclipse period
and release
Latent period Maturation Latent period
(a) (b)
Figure 1.3 Schematic representations of viral growth curves for (a) a nonenveloped virus or an enveloped virus that
acquires its membrane inside the cell (see text) and (b) an enveloped virus that acquires its membrane as it matures
through the plasma membrane. (θ) Intracellular assembly begins at the onset of cell-associated virus detection. (*)
The burst, or lysis of the cell, occurs upon detection of cell-free virus. (b) For viruses that acquire an envelope from the
plasma membrane, the point of release coincides with the point of maturation, and no infectious cell-associated virus is
observed. PFU (plaque-forming unit) is a measure of the amount of infectious units of virus per cell. The coordinates are
labeled only as an example because they will vary with the type of virus.
10 Introduction to virus structure, classification, replication, and hosts
1.3.2 Steps in viral replication more than one type of receptor that depends on the cell
type, whereas others (e.g., HIV) have been shown to require
1.3.2.1 OVERVIEW coreceptors on a single cell type. Furthermore, some viral
There is a general flow of events that occur for virtually all receptors (e.g., sialic acid moieties on host membrane gly-
viruses (Figure 1.4). The early events are (1) attachment, coproteins) are common to many viruses (e.g., influenza
(2) penetration into the cell, and (3) uncoating to release viruses).
genomic material; the middle events are (4) transcription Penetration (entry): Once a virus has successfully attached
of genes to produce mRNA, (5) synthesis of proteins, and to a cell, it must next penetrate the cell’s plasma membrane
(6) replication of genomic material; and the late events to permit the subsequent release of the nucleocapsid and
are (7) assembly to produce mature virions and (8) virion genomic material. Evidence supports three modes of entry
release. These steps may vary greatly with each virus, but (Figure 1.5): (1) Fusion with the plasma membrane (usually
for the sake of simplicity will be discussed in general terms. seen only with enveloped viruses); (2) receptor-mediated
endocytosis, which can be further divided into fusion
1.3.2.2 THE EARLY EVENTS within the endosome or lysis of the endosome; and (3) direct
Attachment: To initiate an infection, a virus must first attach passage through the plasma membrane (usually seen only
to an appropriate host cell. This interaction is mediated by with nonenveloped viruses).
external viral proteins, those found in either the capsid if the Fusion: Fusion is one mechanism of entry employed by
virus is nonenveloped or in the envelope if the virus has a enveloped viruses during which the viral lipid envelope fuses
membrane. Typically, the viral protein binds noncovalently with and then becomes part of the plasma membrane, liber-
in a classic lock-and-key fashion to specific cell surface mac- ating the viral nucleocapsid into the cytoplasm. The fusion
romolecules (either carbohydrates, proteins, or glycolipids) between the membranes is often mediated by fusion proteins
that serve as viral receptors. A virus’s host range can vary found on the surface of the viral envelope. Such an entry
from narrow to broad and is dependent on the presence of strategy is common to retroviruses (e.g., HIV), herpesvi-
viral receptors that dictate species specificity and can even ruses, and paramyxoviruses (e.g., measles virus and mumps
dictate tissue specificity. Some viruses are known to have virus).
Virion
Genomic RNA
1 2 2 3 mRNA
Nucleus
4 Structural protein
Non-structural protein
6
Inclusion
7 body
Assembly
complex 7
8
Figure 1.4 Overview of typical viral replicative cycle for a non-enveloped RNA virus. 1, Attachment; 2, penetration into the
cell; 3, uncoating and release of genomic material; 4, transcription of genes; 5, translation of mRNA and production of viral
proteins; 6, replication of genomic material; 7, assembly and maturation, which can occur within an assembly complex; and
8, cell lysis and virion release. Note that the locations of the various steps will vary depending on the virus type (e.g., her-
pesviruses carry out transcription and replication within the nucleus). Envelope acquisition for enveloped viruses can occur
at intracellular membranes such as the nucleus, or at the plasma membrane upon release. Short wavy lines represent viral
nucleic acid, small triangles represent viral structural proteins that assemble into complexes, and small circles represent
nonstructural proteins that are present within the cell and assist in viral replication and assembly but are not found within
mature virions.
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— Hyvä on nyt häntä etsiä, huokasi Ganimard, — hän on jo
kaukana!
*****
— Jos kunnon Watson nyt näkisi minut, niin kuinka ylpeä hän
olisikaan työtoveristaan! Olihan helppoa arvata, että vihellyksen
kaikuessa taistelu oli menetetty, ja että viisainta oli pitää silmällä
ravintolan ympäristöä. Mutta totta puhuen, elämä on jännittävä kun
on tuon miehen kanssa tekemisissä!
*****
— Arsène Lupinko?
— Niin.
— Ei mitään.
— Niin.
Eteisessä hän teki mutkan astuen kellariin vievän oven luo ja nosti
maasta pienen punaisen kiven: se oli granaatti.
Kun hän ulkona kadulla kääntyi, luki hän numero 40:n seinästä
kirjoituksen: "Lucien Destange, arkkitehti, 1877".
— Oho!
— Ja se päättyy?
— Lupinin vangitsemiseen.
— Niinkö luulette?
Hän katsoi.
*****
Hitto vieköön, hän ajatteli, olenpa minä suuri aasi. Siksi, että
Lupinin ystävätär on vaaleatukkainen ja Clotilde ruskeatukkainen, en
ole ajatellutkaan yhdistää noita naisia! Ikään kuin vaaleatukkainen
nainen voisi pysyä vaaleatukkaisena paroni murhan ja timantin
varastamisen jälkeen!
— Niin kauan kuin nämä kädet ovat minun käteni, tulen olemaan
murheellinen, Maxime.
— Miksikä?
— Ne ovat murhanneet.
Maxime huudahti:
— Mutta?
— Holmesko?
— Sitä paitsi?
— Porttivahtiko?
— Niin.
— Sitä ennen?
— Nyt tiedän, hän sanoi, — salkku M.B. on se, jota etsin. Sen
avulla saan tiedon Lupinin nykyisestä asunnosta.
*****
— Kenelle se on edullista?
— Teille, neiti.
— Puhukaa.
— Samapa se, minä ryhdyn suoraan asiaan. Siis: viisi vuotta sitten
tapasi isänne sattumalta Maxime Bermondin, joka esitteli itsensä
rakennusmestarina… tai arkkitehtina, kumpana, en voi varmasti
sanoa. Pääasia on, että herra Destange mieltyi tähän nuoreen
mieheen ja kun hänen terveydentilansa ei enää sallinut hänen hoitaa
kaikkia yrityksiään, niin uskoi hän herra Bermondin huostaan
muutamien tilausten suorituksen, jotka hän oli ottanut vanhoilta
liiketuttaviltaan vastaan, ja jotka näyttivät soveltuvan hänen uuden
työtoverinsa tehtäviksi.
— Siten, neiti, että herra Maxime Bermondin oikea nimi on, kuten
te tiedätte yhtä hyvin kuin minäkin, Arsène Lupin.
— Te!
— Minäkö?
— Taikka?
— Mitä?
— Hänen kanssarikollisensa?
— Ja sitten?
— Ja sitten?
— Olen.
— Siinäkö kaikki?
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