TABLE OF CONTENTS
An introduction to virology ..........................................................................................................................................................................12
What are viruses?.......................................................................................................................................................................................................... 12
Astonishing number of viruses on Earth à Viruses are everywhere ............................................................................................................................... 12
The human genome contains remnants of viral genetic material .................................................................................................................................... 14
Viruses are small ........................................................................................................................................................................................................... 14
Viruses are diverse in structure ...................................................................................................................................................................................... 14
All viruses are obligatory parasites (they need to get into a cell !) .................................................................................................................................. 15
Virus replication............................................................................................................................................................................................................ 16
Viruses have high genome evolution rates ..................................................................................................................................................................... 17
So, are viruses dead or alive........................................................................................................................................................................................... 18
Most important reasons to exclude viruses from the tree of life ........................................................................................................................................................................................... 18
There are no ancestral viral lineages: ..................................................................................................................................................................................................................................... 18
Viruses don’t have a structure derived from a common ancestor: ......................................................................................................................................................................................... 18
Origin of viruses à Three traditional scenario’s: ............................................................................................................................................................ 19
A typical virus genome à it is a nucleic acid code .......................................................................................................................................................... 20
A chimeric origin of viruses............................................................................................................................................................................................ 20
Five hallmark viral replication genes .............................................................................................................................................................................. 21
Cellular ancestry of capsids............................................................................................................................................................................................ 21
A brief history of virology .............................................................................................................................................................................................. 22
Koch’s postulates !!! to affirm the causes of infectious diseases ...................................................................................................................................... 22
21st century revised version of Koch’s postulates .........................................................................................................................................23
Classification of viruses.................................................................................................................................................................................................. 23
!!!!!!!!! THE BALTIMORE SYSTEM ................................................................................................................................................................................... 24
Definitions/rules underlying the Baltimore system ................................................................................................................................................................................................................ 25
Class I: dsDNA genomes and gapped dsDNA genomes .......................................................................................................................................................................................................... 26
Viruses with dsDNA genomes ................................................................................................................................................................................................................................................ 26
Class II: ssDNA genomes ........................................................................................................................................................................................................................................................ 27
Viruses with ssDNA genomes ................................................................................................................................................................................................................................................. 27
Viruses with RNA genomes .................................................................................................................................................................................................................................................... 27
Class III: dsRNA genomes ....................................................................................................................................................................................................................................................... 28
Viruses with dsRNA genomes ................................................................................................................................................................................................................................................ 28
Class IV: ss(+)RNA genomes ................................................................................................................................................................................................................................................... 28
Class V: ss(-)RNA genomes ..................................................................................................................................................................................................................................................... 29
Class VI: ss(+)RNA genomes with a DNA intermediate ........................................................................................................................................................................................................... 29
Class VII: dsDNA genomes with a RNA intermediate .............................................................................................................................................................................................................. 30
Summary of 7 genome classes according to Baltimore .......................................................................................................................................................................................................... 31
The virology toolbox ...................................................................................................................................................................................33
How can we say that a virus is present or not? ............................................................................................................................................................... 33
Virus isolation and propagation ..................................................................................................................................................................................... 33
Some important definitions and concepts ...................................................................................................................................................................... 33
Virus isolation and propagation in cell culture................................................................................................................................................................ 35
Viruses can induce formation of synctytia ...................................................................................................................................................................... 35
Determining the number of viruses in a sample à 2 main methods ............................................................................................................................... 35
Multiplicity of infection (MOI) ................................................................................................................................................................................................................................................ 37
1
, Physical measurements of virus particles ....................................................................................................................................................................... 38
Electron microscopy ...................................................................................................................................................................................................... 38
Detecting viral antigens and antiviral antibodies ............................................................................................................................................................ 39
introduction part 2: Virus structures ...........................................................................................................................................................40
A typical virus genome .................................................................................................................................................................................................. 40
Virus particles are made up from structural proteins Functions of structural proteins: ........................................................................................................................................................ 40
From larger to smaller blocks................................................................................................................................................................................................................................................. 40
Virus particles are metastable ................................................................................................................................................................................................................................................ 40
3 basic virus structures .......................................................................................................................................................................................................................................................... 41
Symmetry is key to build virus particles Watson and Crick seminal observations: ................................................................................................................................................................ 41
Virus particles are metastable ................................................................................................................................................................................................................................................ 41
Many capsid proteins are self-assembling in VLP (virus-like-particles) ................................................................................................................................................................................... 41
Helical symmetry ........................................................................................................................................................................................................... 42
Icosahedral symmetry (it is like crystals) ........................................................................................................................................................................ 42
Simple icosahedral capsid ...................................................................................................................................................................................................................................................... 42
Capsids can be covered by host-derived lipid membranes (! This is not always) .............................................................................................................. 43
why would a virus get an (extra) envelop (instead of a just capside)? .................................................................................................................................................................................... 43
Viral envelope ............................................................................................................................................................................................................... 44
Viral envelope glycoprotein.................................................................................................................................................................................................................................................... 44
Complex symmetry........................................................................................................................................................................................................ 44
Replication cycles ......................................................................................................................................................................................................... 46
Steps in virus replication ........................................................................................................................................................................................................................................................ 46
Virus attachment and entry ........................................................................................................................................................................................... 46
Cellular receptors for viruses ......................................................................................................................................................................................... 48
Criteria to identify virus receptors à EXAM QUESTION ......................................................................................................................................................................................................... 48
Adhesion receptors and entry receptors ........................................................................................................................................................................ 48
Virus attachment to host glycan polysaccharide ............................................................................................................................................................. 50
Virus attachment to host lectin ...................................................................................................................................................................................... 50
Strategies of how viruses enter cells .............................................................................................................................................................................. 50
Fusion is a regulated process ................................................................................................................................................................................................................................................. 50
Fusion of viral and plasma membranes at the cell surface (receptor mediated) .................................................................................................................................................................... 50
Fusion of virus membrane with host endosomal membrane ................................................................................................................................................................................................. 50
Non-enveloped virus entry and genome release ............................................................................................................................................................ 53
Active transportation through the cytosol ...................................................................................................................................................................... 53
Modes of nuclear entry (mostly DNA viruses) ................................................................................................................................................................ 53
Genome transcription and translation ........................................................................................................................................................................... 55
Some definitions .................................................................................................................................................................................................................................................................... 55
Rules for viral RNA synthesis ......................................................................................................................................................................................... 55
Universal rules for RNA-directed RNA synthesis ............................................................................................................................................................. 55
RdRp initiates RNA synthesis in two ways .............................................................................................................................................................................................................................. 56
Single stranded (+)RNA viruses .............................................................................................................................................................................................................................................. 57
Single stranded (-)RNA viruses ............................................................................................................................................................................................................................................... 57
dsRNA viruses (contain both + and – strands) ........................................................................................................................................................................................................................ 58
dsDNA transcription in DNA viruses ............................................................................................................................................................................... 58
Cap snatching by influenza virus .................................................................................................................................................................................... 59
Viral mRNA’s are polyadenylated at the 3’ end ............................................................................................................................................................... 59
Initiation of translation in eukaryotes ............................................................................................................................................................................ 59
2
, Initiation of translation of uncapped mRNA ................................................................................................................................................................... 59
What does IRES do? .............................................................................................................................................................................................................................................................. 60
Monocistronic and polycistronic mRNA’s ....................................................................................................................................................................... 60
Viruses do all the same things that our proteins do à Post-translational modifications ................................................................................................. 62
Genome replication ...................................................................................................................................................................................................... 64
Locations of virus genome replication in eukaryotic cells ....................................................................................................................................................................................................... 64
Initiation of genome replication ............................................................................................................................................................................................................................................. 64
DNA strand displacement replication ..................................................................................................................................................................................................................................... 66
Key enzymes in RNA virus genome replication ....................................................................................................................................................................................................................... 66
Viral factories......................................................................................................................................................................................................................................................................... 67
ss(-)RNA virus replication (Filoviruses) ................................................................................................................................................................................................................................... 67
Reverse transcription .................................................................................................................................................................................................... 68
introduction part 3 .....................................................................................................................................................................................69
Assembly and exit ......................................................................................................................................................................................................... 69
The structure of a virion determines how it is formed .................................................................................................................................................... 70
All virions complete a common set of assembly reactions .............................................................................................................................................. 70
Moving cargo around the cytoplasm .............................................................................................................................................................................. 70
How to get viral proteins in the right place for assembly? .............................................................................................................................................. 71
Virus assembly is an ordered proces .............................................................................................................................................................................. 71
(Nucleo)capsid assembly and genome packaging ........................................................................................................................................................... 71
Three strategies for making sub-assemblies ................................................................................................................................................................... 72
Some viruses assemble their capsid in the nucleus......................................................................................................................................................... 72
Nuclear exit of the viral genome or nuclear capsid ......................................................................................................................................................... 73
Assisted genome export through nuclear pores..................................................................................................................................................................................................................... 73
Genome export through nuclear egress (Herpesviruses) ....................................................................................................................................................................................................... 74
The particle is then released by exocytosis. ........................................................................................................................................................................................................................... 74
Genome packaging........................................................................................................................................................................................................ 74
Genome packaging signals (RNA genomes)............................................................................................................................................................................................................................ 75
Genome packaging signals (DNA genomes) ........................................................................................................................................................................................................................... 75
Packaging of segmented RNA genomes ................................................................................................................................................................................................................................. 76
Taking along a lipid coat on the way out................................................................................................................................................................................................................................. 76
Virion exit from the cell ................................................................................................................................................................................................. 77
Virus budding through the cellular exocytosis pathway ......................................................................................................................................................................................................... 78
Virus budding at the plasma membrane ................................................................................................................................................................................................................................ 78
Viral budding via host-assisted ESCRT complexes ........................................................................................................................................................... 78
ESCRT-independent budding à exam !! ............................................................................................................................................................................................................................... 78
Cell-to-cell transport...................................................................................................................................................................................................... 79
Virus maturation (example Dengue) ............................................................................................................................................................................. 79
Virus maturation (example HIV) .................................................................................................................................................................................... 79
Virus evolution ...........................................................................................................................................................................................80
Genomic epidemiology of Ebola virus in DRC ................................................................................................................................................................. 80
Genomic epidemiology of SARS-CoV-2 ........................................................................................................................................................................... 80
Phylogenetics ............................................................................................................................................................................................................... 81
Virus evolution and main drivers of evolution ................................................................................................................................................................ 81
RNA virus evolution ............................................................................................................................................................................................................................................................... 81
DNA virus evolution (it is a bit like are our genomes + quite stable) ...................................................................................................................................................................................... 82
3
, The quasispecies concept .............................................................................................................................................................................................. 82
Diversity is selected but also has limits .......................................................................................................................................................................... 84
The error treshold – hypermutation pushed by ribavirin ....................................................................................................................................................................................................... 84
Genetic bottlenecks ............................................................................................................................................................................................................................................................... 84
Genetic bottlenecks in real life ............................................................................................................................................................................................................................................... 85
Avoiding the ‘ratchet’ in real life ............................................................................................................................................................................................................................................ 85
Virus-host arms race...................................................................................................................................................................................................... 86
An experiment in the evolution of virulence .......................................................................................................................................................................................................................... 86
The arms race ........................................................................................................................................................................................................................................................................ 88
Evolution of virulence – more recent examples .............................................................................................................................................................. 88
Virus evolution ...................................................................................................................................................................................................................................................................... 88
Constraints on virus evolution à viral genome cannot change infinitely ............................................................................................................................................................................... 88
In summary................................................................................................................................................................................................................... 89
Emerging & re-emerging viruses .................................................................................................................................................................90
WHO pathogen priority list .................................................................................................................................................................................................................................................... 90
Major drivers of virus emergence and spread ................................................................................................................................................................ 90
Obligate intracellular parasites with small genomes & high mutation rates .................................................................................................................... 92
Zoonotic origin .............................................................................................................................................................................................................. 92
viral hemorrhagic fevers ............................................................................................................................................................................................... 92
Ebolavirus ..................................................................................................................................................................................................................... 93
Ebola virus replication cycle........................................................................................................................................................................................... 95
Clinical course of acute Ebola Virus Disease (slide 16) .................................................................................................................................................... 96
A history of outbreaks in Central Africa.......................................................................................................................................................................... 97
Zoonotic origin of EBOV................................................................................................................................................................................................. 97
Ebola virus genetic diversity and reservoir species?........................................................................................................................................................ 97
Distribution of suspected EBOV-carrying fruit bats ......................................................................................................................................................... 98
Intermediate and/or amplifying host? ........................................................................................................................................................................... 98
Relapse – a new paradigm for starting Ebola virus outbreaks ......................................................................................................................................... 98
The 2013-2016 EBOV outbreak in West Africa ................................................................................................................................................................ 99
VHF outbreak potential in Africa (and beyond) .............................................................................................................................................................. 99
Ebola virus transmission cycles ...................................................................................................................................................................................... 99
Human to human transmission ............................................................................................................................................................................................................................................ 100
Human demographics: Central Africa vs. West Africa ................................................................................................................................................... 100
Extremely weak health care systems & slow response ................................................................................................................................................. 100
2013-2016 EBOV outbreak origin and ignition .............................................................................................................................................................. 101
The 2013-2016 EBOV outbreak evolution ..................................................................................................................................................................... 101
GP A82V mutation – an example of EBOV adaptation to humans ................................................................................................................................. 102
GP A82V confers increased infectivity in human cells ................................................................................................................................................... 102
Association between GP A82V and increased rate of lethal infection............................................................................................................................ 102
A82V sensitizes EBOV GP to activation by the NPC1 receptor… ..................................................................................................................................... 103
…but does not alter pathogenicity in two animal models .................................................................................................................................................................................................... 103
Improvements since the West Africa Ebola outbreak ................................................................................................................................................... 103
Laboratory diagnosis of Ebola virus disease ................................................................................................................................................................. 104
Xpert® Ebola Assay (Cepheid) .............................................................................................................................................................................................................................................. 104
4
An introduction to virology ..........................................................................................................................................................................12
What are viruses?.......................................................................................................................................................................................................... 12
Astonishing number of viruses on Earth à Viruses are everywhere ............................................................................................................................... 12
The human genome contains remnants of viral genetic material .................................................................................................................................... 14
Viruses are small ........................................................................................................................................................................................................... 14
Viruses are diverse in structure ...................................................................................................................................................................................... 14
All viruses are obligatory parasites (they need to get into a cell !) .................................................................................................................................. 15
Virus replication............................................................................................................................................................................................................ 16
Viruses have high genome evolution rates ..................................................................................................................................................................... 17
So, are viruses dead or alive........................................................................................................................................................................................... 18
Most important reasons to exclude viruses from the tree of life ........................................................................................................................................................................................... 18
There are no ancestral viral lineages: ..................................................................................................................................................................................................................................... 18
Viruses don’t have a structure derived from a common ancestor: ......................................................................................................................................................................................... 18
Origin of viruses à Three traditional scenario’s: ............................................................................................................................................................ 19
A typical virus genome à it is a nucleic acid code .......................................................................................................................................................... 20
A chimeric origin of viruses............................................................................................................................................................................................ 20
Five hallmark viral replication genes .............................................................................................................................................................................. 21
Cellular ancestry of capsids............................................................................................................................................................................................ 21
A brief history of virology .............................................................................................................................................................................................. 22
Koch’s postulates !!! to affirm the causes of infectious diseases ...................................................................................................................................... 22
21st century revised version of Koch’s postulates .........................................................................................................................................23
Classification of viruses.................................................................................................................................................................................................. 23
!!!!!!!!! THE BALTIMORE SYSTEM ................................................................................................................................................................................... 24
Definitions/rules underlying the Baltimore system ................................................................................................................................................................................................................ 25
Class I: dsDNA genomes and gapped dsDNA genomes .......................................................................................................................................................................................................... 26
Viruses with dsDNA genomes ................................................................................................................................................................................................................................................ 26
Class II: ssDNA genomes ........................................................................................................................................................................................................................................................ 27
Viruses with ssDNA genomes ................................................................................................................................................................................................................................................. 27
Viruses with RNA genomes .................................................................................................................................................................................................................................................... 27
Class III: dsRNA genomes ....................................................................................................................................................................................................................................................... 28
Viruses with dsRNA genomes ................................................................................................................................................................................................................................................ 28
Class IV: ss(+)RNA genomes ................................................................................................................................................................................................................................................... 28
Class V: ss(-)RNA genomes ..................................................................................................................................................................................................................................................... 29
Class VI: ss(+)RNA genomes with a DNA intermediate ........................................................................................................................................................................................................... 29
Class VII: dsDNA genomes with a RNA intermediate .............................................................................................................................................................................................................. 30
Summary of 7 genome classes according to Baltimore .......................................................................................................................................................................................................... 31
The virology toolbox ...................................................................................................................................................................................33
How can we say that a virus is present or not? ............................................................................................................................................................... 33
Virus isolation and propagation ..................................................................................................................................................................................... 33
Some important definitions and concepts ...................................................................................................................................................................... 33
Virus isolation and propagation in cell culture................................................................................................................................................................ 35
Viruses can induce formation of synctytia ...................................................................................................................................................................... 35
Determining the number of viruses in a sample à 2 main methods ............................................................................................................................... 35
Multiplicity of infection (MOI) ................................................................................................................................................................................................................................................ 37
1
, Physical measurements of virus particles ....................................................................................................................................................................... 38
Electron microscopy ...................................................................................................................................................................................................... 38
Detecting viral antigens and antiviral antibodies ............................................................................................................................................................ 39
introduction part 2: Virus structures ...........................................................................................................................................................40
A typical virus genome .................................................................................................................................................................................................. 40
Virus particles are made up from structural proteins Functions of structural proteins: ........................................................................................................................................................ 40
From larger to smaller blocks................................................................................................................................................................................................................................................. 40
Virus particles are metastable ................................................................................................................................................................................................................................................ 40
3 basic virus structures .......................................................................................................................................................................................................................................................... 41
Symmetry is key to build virus particles Watson and Crick seminal observations: ................................................................................................................................................................ 41
Virus particles are metastable ................................................................................................................................................................................................................................................ 41
Many capsid proteins are self-assembling in VLP (virus-like-particles) ................................................................................................................................................................................... 41
Helical symmetry ........................................................................................................................................................................................................... 42
Icosahedral symmetry (it is like crystals) ........................................................................................................................................................................ 42
Simple icosahedral capsid ...................................................................................................................................................................................................................................................... 42
Capsids can be covered by host-derived lipid membranes (! This is not always) .............................................................................................................. 43
why would a virus get an (extra) envelop (instead of a just capside)? .................................................................................................................................................................................... 43
Viral envelope ............................................................................................................................................................................................................... 44
Viral envelope glycoprotein.................................................................................................................................................................................................................................................... 44
Complex symmetry........................................................................................................................................................................................................ 44
Replication cycles ......................................................................................................................................................................................................... 46
Steps in virus replication ........................................................................................................................................................................................................................................................ 46
Virus attachment and entry ........................................................................................................................................................................................... 46
Cellular receptors for viruses ......................................................................................................................................................................................... 48
Criteria to identify virus receptors à EXAM QUESTION ......................................................................................................................................................................................................... 48
Adhesion receptors and entry receptors ........................................................................................................................................................................ 48
Virus attachment to host glycan polysaccharide ............................................................................................................................................................. 50
Virus attachment to host lectin ...................................................................................................................................................................................... 50
Strategies of how viruses enter cells .............................................................................................................................................................................. 50
Fusion is a regulated process ................................................................................................................................................................................................................................................. 50
Fusion of viral and plasma membranes at the cell surface (receptor mediated) .................................................................................................................................................................... 50
Fusion of virus membrane with host endosomal membrane ................................................................................................................................................................................................. 50
Non-enveloped virus entry and genome release ............................................................................................................................................................ 53
Active transportation through the cytosol ...................................................................................................................................................................... 53
Modes of nuclear entry (mostly DNA viruses) ................................................................................................................................................................ 53
Genome transcription and translation ........................................................................................................................................................................... 55
Some definitions .................................................................................................................................................................................................................................................................... 55
Rules for viral RNA synthesis ......................................................................................................................................................................................... 55
Universal rules for RNA-directed RNA synthesis ............................................................................................................................................................. 55
RdRp initiates RNA synthesis in two ways .............................................................................................................................................................................................................................. 56
Single stranded (+)RNA viruses .............................................................................................................................................................................................................................................. 57
Single stranded (-)RNA viruses ............................................................................................................................................................................................................................................... 57
dsRNA viruses (contain both + and – strands) ........................................................................................................................................................................................................................ 58
dsDNA transcription in DNA viruses ............................................................................................................................................................................... 58
Cap snatching by influenza virus .................................................................................................................................................................................... 59
Viral mRNA’s are polyadenylated at the 3’ end ............................................................................................................................................................... 59
Initiation of translation in eukaryotes ............................................................................................................................................................................ 59
2
, Initiation of translation of uncapped mRNA ................................................................................................................................................................... 59
What does IRES do? .............................................................................................................................................................................................................................................................. 60
Monocistronic and polycistronic mRNA’s ....................................................................................................................................................................... 60
Viruses do all the same things that our proteins do à Post-translational modifications ................................................................................................. 62
Genome replication ...................................................................................................................................................................................................... 64
Locations of virus genome replication in eukaryotic cells ....................................................................................................................................................................................................... 64
Initiation of genome replication ............................................................................................................................................................................................................................................. 64
DNA strand displacement replication ..................................................................................................................................................................................................................................... 66
Key enzymes in RNA virus genome replication ....................................................................................................................................................................................................................... 66
Viral factories......................................................................................................................................................................................................................................................................... 67
ss(-)RNA virus replication (Filoviruses) ................................................................................................................................................................................................................................... 67
Reverse transcription .................................................................................................................................................................................................... 68
introduction part 3 .....................................................................................................................................................................................69
Assembly and exit ......................................................................................................................................................................................................... 69
The structure of a virion determines how it is formed .................................................................................................................................................... 70
All virions complete a common set of assembly reactions .............................................................................................................................................. 70
Moving cargo around the cytoplasm .............................................................................................................................................................................. 70
How to get viral proteins in the right place for assembly? .............................................................................................................................................. 71
Virus assembly is an ordered proces .............................................................................................................................................................................. 71
(Nucleo)capsid assembly and genome packaging ........................................................................................................................................................... 71
Three strategies for making sub-assemblies ................................................................................................................................................................... 72
Some viruses assemble their capsid in the nucleus......................................................................................................................................................... 72
Nuclear exit of the viral genome or nuclear capsid ......................................................................................................................................................... 73
Assisted genome export through nuclear pores..................................................................................................................................................................................................................... 73
Genome export through nuclear egress (Herpesviruses) ....................................................................................................................................................................................................... 74
The particle is then released by exocytosis. ........................................................................................................................................................................................................................... 74
Genome packaging........................................................................................................................................................................................................ 74
Genome packaging signals (RNA genomes)............................................................................................................................................................................................................................ 75
Genome packaging signals (DNA genomes) ........................................................................................................................................................................................................................... 75
Packaging of segmented RNA genomes ................................................................................................................................................................................................................................. 76
Taking along a lipid coat on the way out................................................................................................................................................................................................................................. 76
Virion exit from the cell ................................................................................................................................................................................................. 77
Virus budding through the cellular exocytosis pathway ......................................................................................................................................................................................................... 78
Virus budding at the plasma membrane ................................................................................................................................................................................................................................ 78
Viral budding via host-assisted ESCRT complexes ........................................................................................................................................................... 78
ESCRT-independent budding à exam !! ............................................................................................................................................................................................................................... 78
Cell-to-cell transport...................................................................................................................................................................................................... 79
Virus maturation (example Dengue) ............................................................................................................................................................................. 79
Virus maturation (example HIV) .................................................................................................................................................................................... 79
Virus evolution ...........................................................................................................................................................................................80
Genomic epidemiology of Ebola virus in DRC ................................................................................................................................................................. 80
Genomic epidemiology of SARS-CoV-2 ........................................................................................................................................................................... 80
Phylogenetics ............................................................................................................................................................................................................... 81
Virus evolution and main drivers of evolution ................................................................................................................................................................ 81
RNA virus evolution ............................................................................................................................................................................................................................................................... 81
DNA virus evolution (it is a bit like are our genomes + quite stable) ...................................................................................................................................................................................... 82
3
, The quasispecies concept .............................................................................................................................................................................................. 82
Diversity is selected but also has limits .......................................................................................................................................................................... 84
The error treshold – hypermutation pushed by ribavirin ....................................................................................................................................................................................................... 84
Genetic bottlenecks ............................................................................................................................................................................................................................................................... 84
Genetic bottlenecks in real life ............................................................................................................................................................................................................................................... 85
Avoiding the ‘ratchet’ in real life ............................................................................................................................................................................................................................................ 85
Virus-host arms race...................................................................................................................................................................................................... 86
An experiment in the evolution of virulence .......................................................................................................................................................................................................................... 86
The arms race ........................................................................................................................................................................................................................................................................ 88
Evolution of virulence – more recent examples .............................................................................................................................................................. 88
Virus evolution ...................................................................................................................................................................................................................................................................... 88
Constraints on virus evolution à viral genome cannot change infinitely ............................................................................................................................................................................... 88
In summary................................................................................................................................................................................................................... 89
Emerging & re-emerging viruses .................................................................................................................................................................90
WHO pathogen priority list .................................................................................................................................................................................................................................................... 90
Major drivers of virus emergence and spread ................................................................................................................................................................ 90
Obligate intracellular parasites with small genomes & high mutation rates .................................................................................................................... 92
Zoonotic origin .............................................................................................................................................................................................................. 92
viral hemorrhagic fevers ............................................................................................................................................................................................... 92
Ebolavirus ..................................................................................................................................................................................................................... 93
Ebola virus replication cycle........................................................................................................................................................................................... 95
Clinical course of acute Ebola Virus Disease (slide 16) .................................................................................................................................................... 96
A history of outbreaks in Central Africa.......................................................................................................................................................................... 97
Zoonotic origin of EBOV................................................................................................................................................................................................. 97
Ebola virus genetic diversity and reservoir species?........................................................................................................................................................ 97
Distribution of suspected EBOV-carrying fruit bats ......................................................................................................................................................... 98
Intermediate and/or amplifying host? ........................................................................................................................................................................... 98
Relapse – a new paradigm for starting Ebola virus outbreaks ......................................................................................................................................... 98
The 2013-2016 EBOV outbreak in West Africa ................................................................................................................................................................ 99
VHF outbreak potential in Africa (and beyond) .............................................................................................................................................................. 99
Ebola virus transmission cycles ...................................................................................................................................................................................... 99
Human to human transmission ............................................................................................................................................................................................................................................ 100
Human demographics: Central Africa vs. West Africa ................................................................................................................................................... 100
Extremely weak health care systems & slow response ................................................................................................................................................. 100
2013-2016 EBOV outbreak origin and ignition .............................................................................................................................................................. 101
The 2013-2016 EBOV outbreak evolution ..................................................................................................................................................................... 101
GP A82V mutation – an example of EBOV adaptation to humans ................................................................................................................................. 102
GP A82V confers increased infectivity in human cells ................................................................................................................................................... 102
Association between GP A82V and increased rate of lethal infection............................................................................................................................ 102
A82V sensitizes EBOV GP to activation by the NPC1 receptor… ..................................................................................................................................... 103
…but does not alter pathogenicity in two animal models .................................................................................................................................................................................................... 103
Improvements since the West Africa Ebola outbreak ................................................................................................................................................... 103
Laboratory diagnosis of Ebola virus disease ................................................................................................................................................................. 104
Xpert® Ebola Assay (Cepheid) .............................................................................................................................................................................................................................................. 104
4
