Table of contents
Table of contents ..................................................................................................................................... 1
Basics infectious diseases ........................................................................................................................ 3
Innate and adaptive response ................................................................................................................. 7
Innate immunity and defenses of the body .................................................................................... 7
Adaptive immune responses ........................................................................................................... 8
Virus background, classification and diagnostics .................................................................................. 10
Laboratory diagnostics ...................................................................................................................... 12
Direct methods: ............................................................................................................................. 13
Indirect methods ........................................................................................................................... 15
Mosquito borne infection ..................................................................................................................... 17
Flaviviruses .................................................................................................................................... 17
Togavirus ....................................................................................................................................... 19
Arboviruses ........................................................................................................................................ 20
Yellow fever ................................................................................................................................... 21
Dengue fever ................................................................................................................................. 22
Zika virus ........................................................................................................................................ 23
Chikungunya virus infection (CHIKV) ............................................................................................. 23
Arthropod vectors ......................................................................................................................... 24
Viral respiratory tract infection (incl. vaccines) .................................................................................... 25
Influenza/ negative RNA viruses........................................................................................................ 25
Influenza A virus (IAV) ................................................................................................................... 25
Corona virus ...................................................................................................................................... 30
Principles of vaccination ................................................................................................................ 33
Vaccines ................................................................................................................................................. 34
Vaccine development .................................................................................................................... 38
HIV-1 and DNA viruses .......................................................................................................................... 40
Molecular virology of HIV/ retroviruses ........................................................................................ 40
AIDS ............................................................................................................................................... 44
Interactive lecture ......................................................................................................................... 45
HIV immunity and pathogenesis ................................................................................................... 46
DNA Virus ...................................................................................................................................... 49
Herpesvirus.................................................................................................................................... 49
Bacterial respiratory and gastro-intestinal tract ................................................................................... 54
Tuberculosis................................................................................................................................... 54
, Heamophilus influenza .................................................................................................................. 57
Heamophilus meningitis ................................................................................................................ 57
Non-typable Heamophilus influenzae ........................................................................................... 58
Neisseria meningitis ...................................................................................................................... 59
Meningococcal meningitis ............................................................................................................. 60
Whooping cough (Bordetella pertussis) ........................................................................................ 61
Pneumococcal infections............................................................................................................... 64
Gastrointestinal bacterial and viral infections ...................................................................................... 70
Sexually transmitted diseases and Sepsis ............................................................................................. 81
Sexually transmitted bacterial infections .......................................................................................... 81
Syfilis .............................................................................................................................................. 81
Gonorrhoeae caused by Neisseria gonorrhoeae........................................................................... 81
Chlamydia caused by Chlamydia trachomatis ............................................................................... 82
Neonatal sepsis.............................................................................................................................. 83
Sexually transmitted viral infections ................................................................................................. 86
Hepatitis B ..................................................................................................................................... 86
Human papilloma virus (HPV) ....................................................................................................... 87
Sepsis ............................................................................................................................................. 89
Parasitic infection (malaria)................................................................................................................... 91
Malaria treatment and resistance ................................................................................................. 91
Antimalarials action & resistance .................................................................................................. 93
Fungal infections ................................................................................................................................... 96
Fungal diseases .............................................................................................................................. 96
Multidrug resistance in Aspergillus fumigatus .............................................................................. 99
Immunity against fungal infections ............................................................................................. 100
,Basics infectious diseases
Overview of infected diseases transmitted by arthropods
Most viruses have a cellular organization, being made up of single cells (most ‘microbes’) or of many cells. Each
cell has genetic material (DNA) and cytoplasm with synthetic machinery, and is bounded by a cell membrane.
Bacteria are prokaryotes; all other organisms are eukaryotes.
Differences prokaryotes and eukaryotes
In eukaryotes: transcription and translation are carried out separately with transcribed messenger RNA (mRNA)
moving out of the nucleus into the cytoplasm for ribosomal translation
In prokaryotes: DNA is in the form of a single circular chromosome; additional ‘extrachromosomal’ DNA is carried
in plasmids. Transcription and translation can be carried out simultaneously.
Gram-negative bacteria
- Have an outer lipopolysaccharide-rich layer
- A thick protective cell wall
- In Gram-positive bacteria this wall, made of peptidoglycan, forms the external surface of the cell,
whereas in Gram-negative bacteria there is an additional outer layer rich in lipopolysaccharides. These
, layers play an important role in protecting the cell against the host immune system and
chemotherapeutic agents, and in stimulating certain pathological responses.
Pathogens within cells are protected from many of the host’s defence mechanisms
Pathogens that live within cells are largely protected against many of the host’s defence mechanisms while they
remain there, particularly against the action of specific antibodies. Control of these infections depends therefore
on the activities of intracellular killing mechanisms, short-range mediators or cytotoxic agents, although the
latter may destroy both the pathogen and the host cell, leading to tissue damage. This problem, of targeting
activity against the pathogen when it lives within a vulnerable cell, also arises when using drugs or antibiotics, as
it is difficult to achieve selective action against the pathogen while leaving the host cell intact. Even more
problematic is the fact that many intracellular pathogens live inside the very cells responsible for the host’s
immune and inflammatory mechanisms and therefore depress the host’s defensive abilities. For example, a
variety of viral, bacterial and protozoal pathogens live inside macrophages, and several viruses (including human
immunodeficiency virus, HIV) are specific for lymphocytes.
Living outside cells provides opportunities for growth, reproduction and dissemination
Many extracellular pathogens have the ability to spread rapidly through extracellular fluids or to move rapidly
over surfaces, resulting in a widespread infection within a relatively short time. The rapid colonization of the
entire mucosal surface of the small bowel by Vibrio cholerae is a good example. Successful host defense against
extracellular parasites requires mechanisms that differ from those used in defense against intracellular parasites.
Viruses
- All viruses make mRNA that can be read by host ribosomes. Virus replicates only in the host (inside the
cell). Virus particles do not grow or divide. First the components are made and then they assemble.
- + strand RNA will directly go to the mRNa (directly translated)
- And first needs to make a positive strand (converted into +) (virus brings their own polymerase to do
this)
- Viruses within a family do not always cause the same disease, viruses in different families can cause
the same disease.
- The genetic material, in the form of single-stranded (ss) or double-stranded (ds), linear or circular RNA
or DNA, is contained within a coat or capsid, made up of a number of individual protein molecules
(capsomeres).
- The complete unit of nucleic acid and capsid is called the ‘nucleocapsid’, and often has a distinctive
symmetry depending upon the ways in which the individual capsomeres are assembled (Fig. 3.1).
Symmetry can be icosahedral, helical or complex.
- In many cases, the entire virus particle or ‘virion’ consists only of a nucleocapsid. In others, the virion
consists of the nucleocapsid surrounded by an outer envelope or membrane (Fig. 3.2). This is generally
a lipid bilayer of host cell origin, into which virus proteins and glycoproteins are inserted.
Stages in the infection of a host’s cell and replication of a virus. Several thousand virus particles may be formed
from each cell.
Table of contents ..................................................................................................................................... 1
Basics infectious diseases ........................................................................................................................ 3
Innate and adaptive response ................................................................................................................. 7
Innate immunity and defenses of the body .................................................................................... 7
Adaptive immune responses ........................................................................................................... 8
Virus background, classification and diagnostics .................................................................................. 10
Laboratory diagnostics ...................................................................................................................... 12
Direct methods: ............................................................................................................................. 13
Indirect methods ........................................................................................................................... 15
Mosquito borne infection ..................................................................................................................... 17
Flaviviruses .................................................................................................................................... 17
Togavirus ....................................................................................................................................... 19
Arboviruses ........................................................................................................................................ 20
Yellow fever ................................................................................................................................... 21
Dengue fever ................................................................................................................................. 22
Zika virus ........................................................................................................................................ 23
Chikungunya virus infection (CHIKV) ............................................................................................. 23
Arthropod vectors ......................................................................................................................... 24
Viral respiratory tract infection (incl. vaccines) .................................................................................... 25
Influenza/ negative RNA viruses........................................................................................................ 25
Influenza A virus (IAV) ................................................................................................................... 25
Corona virus ...................................................................................................................................... 30
Principles of vaccination ................................................................................................................ 33
Vaccines ................................................................................................................................................. 34
Vaccine development .................................................................................................................... 38
HIV-1 and DNA viruses .......................................................................................................................... 40
Molecular virology of HIV/ retroviruses ........................................................................................ 40
AIDS ............................................................................................................................................... 44
Interactive lecture ......................................................................................................................... 45
HIV immunity and pathogenesis ................................................................................................... 46
DNA Virus ...................................................................................................................................... 49
Herpesvirus.................................................................................................................................... 49
Bacterial respiratory and gastro-intestinal tract ................................................................................... 54
Tuberculosis................................................................................................................................... 54
, Heamophilus influenza .................................................................................................................. 57
Heamophilus meningitis ................................................................................................................ 57
Non-typable Heamophilus influenzae ........................................................................................... 58
Neisseria meningitis ...................................................................................................................... 59
Meningococcal meningitis ............................................................................................................. 60
Whooping cough (Bordetella pertussis) ........................................................................................ 61
Pneumococcal infections............................................................................................................... 64
Gastrointestinal bacterial and viral infections ...................................................................................... 70
Sexually transmitted diseases and Sepsis ............................................................................................. 81
Sexually transmitted bacterial infections .......................................................................................... 81
Syfilis .............................................................................................................................................. 81
Gonorrhoeae caused by Neisseria gonorrhoeae........................................................................... 81
Chlamydia caused by Chlamydia trachomatis ............................................................................... 82
Neonatal sepsis.............................................................................................................................. 83
Sexually transmitted viral infections ................................................................................................. 86
Hepatitis B ..................................................................................................................................... 86
Human papilloma virus (HPV) ....................................................................................................... 87
Sepsis ............................................................................................................................................. 89
Parasitic infection (malaria)................................................................................................................... 91
Malaria treatment and resistance ................................................................................................. 91
Antimalarials action & resistance .................................................................................................. 93
Fungal infections ................................................................................................................................... 96
Fungal diseases .............................................................................................................................. 96
Multidrug resistance in Aspergillus fumigatus .............................................................................. 99
Immunity against fungal infections ............................................................................................. 100
,Basics infectious diseases
Overview of infected diseases transmitted by arthropods
Most viruses have a cellular organization, being made up of single cells (most ‘microbes’) or of many cells. Each
cell has genetic material (DNA) and cytoplasm with synthetic machinery, and is bounded by a cell membrane.
Bacteria are prokaryotes; all other organisms are eukaryotes.
Differences prokaryotes and eukaryotes
In eukaryotes: transcription and translation are carried out separately with transcribed messenger RNA (mRNA)
moving out of the nucleus into the cytoplasm for ribosomal translation
In prokaryotes: DNA is in the form of a single circular chromosome; additional ‘extrachromosomal’ DNA is carried
in plasmids. Transcription and translation can be carried out simultaneously.
Gram-negative bacteria
- Have an outer lipopolysaccharide-rich layer
- A thick protective cell wall
- In Gram-positive bacteria this wall, made of peptidoglycan, forms the external surface of the cell,
whereas in Gram-negative bacteria there is an additional outer layer rich in lipopolysaccharides. These
, layers play an important role in protecting the cell against the host immune system and
chemotherapeutic agents, and in stimulating certain pathological responses.
Pathogens within cells are protected from many of the host’s defence mechanisms
Pathogens that live within cells are largely protected against many of the host’s defence mechanisms while they
remain there, particularly against the action of specific antibodies. Control of these infections depends therefore
on the activities of intracellular killing mechanisms, short-range mediators or cytotoxic agents, although the
latter may destroy both the pathogen and the host cell, leading to tissue damage. This problem, of targeting
activity against the pathogen when it lives within a vulnerable cell, also arises when using drugs or antibiotics, as
it is difficult to achieve selective action against the pathogen while leaving the host cell intact. Even more
problematic is the fact that many intracellular pathogens live inside the very cells responsible for the host’s
immune and inflammatory mechanisms and therefore depress the host’s defensive abilities. For example, a
variety of viral, bacterial and protozoal pathogens live inside macrophages, and several viruses (including human
immunodeficiency virus, HIV) are specific for lymphocytes.
Living outside cells provides opportunities for growth, reproduction and dissemination
Many extracellular pathogens have the ability to spread rapidly through extracellular fluids or to move rapidly
over surfaces, resulting in a widespread infection within a relatively short time. The rapid colonization of the
entire mucosal surface of the small bowel by Vibrio cholerae is a good example. Successful host defense against
extracellular parasites requires mechanisms that differ from those used in defense against intracellular parasites.
Viruses
- All viruses make mRNA that can be read by host ribosomes. Virus replicates only in the host (inside the
cell). Virus particles do not grow or divide. First the components are made and then they assemble.
- + strand RNA will directly go to the mRNa (directly translated)
- And first needs to make a positive strand (converted into +) (virus brings their own polymerase to do
this)
- Viruses within a family do not always cause the same disease, viruses in different families can cause
the same disease.
- The genetic material, in the form of single-stranded (ss) or double-stranded (ds), linear or circular RNA
or DNA, is contained within a coat or capsid, made up of a number of individual protein molecules
(capsomeres).
- The complete unit of nucleic acid and capsid is called the ‘nucleocapsid’, and often has a distinctive
symmetry depending upon the ways in which the individual capsomeres are assembled (Fig. 3.1).
Symmetry can be icosahedral, helical or complex.
- In many cases, the entire virus particle or ‘virion’ consists only of a nucleocapsid. In others, the virion
consists of the nucleocapsid surrounded by an outer envelope or membrane (Fig. 3.2). This is generally
a lipid bilayer of host cell origin, into which virus proteins and glycoproteins are inserted.
Stages in the infection of a host’s cell and replication of a virus. Several thousand virus particles may be formed
from each cell.
