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Viral evolution, some economic approaches
Viral evolution, some economic approaches
Viral evolution, some economic approaches
Viral evolution, some economic approaches
... “the phenomenon of constructing, destroying, or altering one’s
environment and thus changing the selection pressures exerted by that
environment.”




                                           Boni and Feldman, 2005
Populations of
       t     Et     Natural selection
                                        Gene                       diverse
                                        pool                     phenotypes




                                          Genetic inheritance
time




                                                                Populations of
                                        Gene
       t+1   Et+1   Natural selection   pool
                                                                   diverse
                                                                 phenotypes
Niche construction                           Populations of
       t     Et                        Natural selection
                                                            Gene                       diverse
                                                            pool                     phenotypes




              Ecological inheritance




                                                              Genetic inheritance
time




                                       Niche construction                           Populations of
                                                            Gene
       t+1   Et+1                      Natural selection    pool
                                                                                       diverse
                                                                                     phenotypes
Embioptera
                                                                                                       Synbranchiformes
                                                                               Sarcophagids Swallows Helicopsychidae

                             Fungi                                                   Ptilonorhynchidae
                                                                              Mosses Uropeltidae                   Termites
                                                                                  Birds                                                    Apodidae                          House martin
                                Dipodidae Kingfishers                                                               Bees                    Milkweed
                                                                                                                                                                            Trochilidae
                                                                                                                                                                           Vombatidae
                                           Ophichthidae
                           Alligators Cyanobacteria Chameleons Lampreys                                     River otters   Beavers Gastercantha




                                                                                                                                                                                                      Myrmeleontidae
                                                                                       Gecko                                   Hydropsychiade
                               Amphibians         Cassava Red admiral Testudinata
                                                 Cyclosa Iguanas             Lycosidae
                                                                                          Rhynchocephalia Acacia               Blattodea
                      Pipesnakes Toadfish                                                                  Myctophidae
                                           Chiromantis




                                                                                                                                                                                                                       Worms
                                                              Bathyergidae
                                                                             Crocodiles Sandpipers
            Apicotermes
                                 Lizards     Ctenizidae Opossum Bombyliidae
                    Testudinidae Merganser Siluriformes Wren Symphyta Drosophila
                                                                                                Stomiiformes Smelts
                                                                                                              Turkeys
                                                                                                                                      Isopods
              Membracidae                                                                                    Black rush

                                                                                                             Beetles
                                                                                                                                      Psocoptera
                                                                 Mallos Marmots




                                                                         Euchondrus
           Cynomys Gasterosteus                  Tenebrionidae




                                                                   Pongidae
                                                                                                                    Galliwasps
         Honey eater Rabbits Zebras              Bembix Areneus Tuna
                                                                                                                Homo




                                                                                                                                                                                                 Ergot fungus
                        Philopotamidae            Crustaceans Flatworms Sphagnum Oviparous insects
                                                                                                                                                                                                                       Finch




                                                             Congridae




                                                                                                                                                                                                   Melinae
            Alcedinidae Hirundinidae
                                                                                                        Mammals
                           Ant lions                Snake eels Atta                                      Vanessa
   Hamsters Sharks




                              Parus
                               Peromyscus         Owls Scolytidae                                 Parasitoid insects            Cricitelus
           Galaxids          Liphistiidae      Eublepharidae         Coniosporium Momotidae Muskrats Eider duck                 Hemiptera Algae




    Capitonidae
                                                                                                                                                                                 Plants
                Buffalo grass Petrel Periophthalmus Uloborus  Turdus Tuatara Teiidae
                                                                                           Tephritid flies                              Paelobatidae
                            Meropidae                                 Lanternfishes         Passalidae




              Badgers
                 Sauria                         Chaparral Swifts Coral Mudskippers Gerbils                                                 Animalia
                Millipedes Grasses Moths            Dolphins Snails Gryllotalpidae                                                      Vulpes
             Weeverfishes Ploceidae Malaria
                                                                                        Ichneumonidae
                                                                         Batrachoididae Ensiferan Cormorants Scombridae Tortoise Tachyoryctes
                  Macronema Theridion Mosquitoes Dragonfishes                                         Wombats Spalax            Hornbills
                                       Typhlopidae




                                                                                                          DiatomsLichens




                                                                                                                                                                                                                                                  Snakes Bowerbirds
                                                                                       Mole rats




                                                                                                                                                         Deinopidae
                                                                            Ostariophysi Rooks
       Caecilians Bucerotidae Pleurodira                                                                    Macrotermitinae Microhylidae
                                                                            Rodents Pisauridae              Catfish Prairie dogs




                                                                                                                                                                      Jerboas
                                Puffinus
        Scarabaeidae Cows Moles Anguillidae                Cyclorana          Paradise fish Carp
             Limnephilidae                          Rats Salmon                Coleoptera Thrush          Protists Pythons
                                                                     Cattle                                                                                                                                             Frogs




                                                Eucalyptus
 Argyroneta Caelifera Flies




                                                                                                                                                                                Wasps
                                         Tits
    Lobsters                                          Snapping shrimps Reithrodontomys                               Turtles
              Cuckoo Squirrels Earwigs HedgehogsKatydids Guinea pigs                              Osmeridae           Hirundines




                                                                                                                                                                                Magpies
                                                                      Lutra       Dibamids                             Lepidoptera Eels




                                                                                                                                            Chiroptera
Trachinoidei Ovenbirds Lovebirds Louse Neanderthals Bats                      Cichlids             Viruses
                                                                                                 Agapornis
                                                           Caterpillars                                                   Porcupines
           Erinaceus Amphipods
                                                                Reptiles
                                                             Trionychidae Gazelles   Mites




                                                                                                                                                                                                                                            Vertebrates
                                                                                                                       Characiformes
        Gymnopphiona Eumenidae Barbets                                                            Bark lice         Voles     Primates
                                 Beeflies                 Cavia Trichoptera
                                                                                                 Silverfish VespinaeFishes
                                                                                                                         Dipterans




                                                                                                                                                                                Whales
                                Cicadas Wildebeest Weaverbirds Cod
                            Trees
        Braunsapis

                                                                                        Bacteria
                                                                                                               Helodermatidae




                                                                                                                                                                                                                                     Polistinae
                                                                                             Braconidae
             Archaebacteria Chough Beech trees                                   Leptotyphlopidae                  Microphytes




                                                                                                                                                                                                                          Petromyzontiformes
    Hemisotidae Terrapins Foxes Eubacteria



                                          Spiders
                                             Guppies                            Megapodes Aniliidae Amphisbaenia Vipes
                  Picidae                                                              Locusts Tapinillus         Basidiomycetes
             Furnariidae Storks                                                             Viceroy Teleutomyrmex




                                                                                                                                                                                                      Insects
            Scincidae
                   Thysanoptera                                                         Treehoppers Corvids Acrididae
                         Eagles                                                        Zooplankton        Clupeiformes
                         Mouthbrooder                                                                                             Monarch butterfly
                        Tetragnatha

                                                                                Hominids
                                                                                                                                             Skinks                             Orthoptera




                                                                                                                               Segestria
                                      Pine trees                                                                                           Gophers                    Apinae




                                                                                                                                                                                          Arachnids
                         Dendrobatidae   Dermaptera                                                                                              Segestriidae




                                                                                                                                                                                    Sawflies
                                            Grasshoppers                                          Flowering plants                  Pygopodids




                                                                                                                                                                                   Motmots
                                                                                       Hystrix
                           Butterflies Lemmings                                                   Nile monitor              Bee eaters Sardines
                                                                                      Epiphytes
                                                                                  Hummingbirds
                                                                                      Ariadna Gobies
                                                                                                     Rhinophrynidae
                                                                   Anomalepididae
                                                                                                   Painted lady


                                                                                                  Ants
                                                                                                                           Stickelback
                                                                      Woodpeckers                                              Sea turtle
                                         Hymenoptera
histiidae      Eublepharidae       Coniosporium Momotidae Muskrats Eider duck    Hemiptera

                                                                                                   Plants
                             Turdus Tuatara Teiidae




                                                                                                            E
Petrel Periophthalmus Uloborus                       Tephritid flies                     Pa
 pidae          Chaparral Swifts    Lanternfishes     Passalidae                           A
asses    Moths                  Coral  Mudskippers    Gerbils                            Vu
ceidae   MalariaDolphins Snails BatrachoididaeIchneumonidae
                               Gryllotalpidae
                                                            Cormorants Scombridae Tortoise
 Theridion Mosquitoes Dragonfishes               Ensiferan Wombats Spalax        Hornbills
     Typhlopidae




                                                Lichens
                              Mole rats




                                                                           Deinopidae
                                       Ostariophysi Rooks
 ae
                                                Pisauridae        Macrotermitinae Microhyl
                                           Rodents                       Catfish Prairie dogs




                                                                                        Jerboas
uffinus Pleurodira
Moles AnguillidaeRats Cyclorana             Paradise fish Carp
                           Salmon            Coleoptera Thrush         Protists Pythons
                         Cattle                                                                                 Frog
           Eucalyptus




                                                                                                  Wasps
    Tits




                       Snapping shrimps Reithrodontomys                           Turtles



                                        Diatoms
rrels     Earwigs Hedgehogs Katydids Guinea pigs               Osmeridae           Hirundines




                                                                                                  Magpies
                                     Lutra      Dibamids                            Lepidoptera Eels




                                                              Chiroptera
ebirds Louse    Neanderthals Bats           Cichlids            Viruses
                           Caterpillars                       Agapornis                Porcupines
pods
 menidae                Reptiles
                            Trionychidae  Gazelles Mites Bark lice                  Characiformes
                                                                                 Voles     Primates
 Beeflies Barbets         Cavia Trichoptera
                                                  Fishes                    VespinaeDipterans




                                                                                                  Whales
 icadas Wildebeest  Weaverbirds Cod                           Silverfish

                                  Bacteria
                                                                            Helodermatidae




                                                                                                                       Polistinae
                                                          Braconidae
Chough Beech trees                             Leptotyphlopidae                 Microphytes




                                                                                                                omyzontiformes
            Eubacteria
Foxes         Guppies                         Megapodes Aniliidae Amphisbaenia Vipes
                                                     Locusts Tapinillus        Basidiomycetes
                                                             Viceroy                     Teleutomyrmex




                                                                                                            ts
a                                                          Treehoppers Corvids Acrididae
                                                          Zooplankton    Clupeiformes
Viral evolution, some economic approaches
Viral evolution, some economic approaches
Viral evolution, some economic approaches
Why manipulate the host so dramatically?




            How do such manipulations arise?




How do niche effects outside the host affect the virus?
Viral evolution, some economic approaches
Baculoviruses


                               Nucleopolyhedrovirus                         the point where they are unrecognisable or whe
                                      (NPV)                                 have lost the genes entirely. There is some data to
    MNPV                                                                    that the hymenopteran viruses may not spread be
                                                                            midgut, in which case a budded virus (BV) form m
                                                                            necessary (Duffy et al., 2006). The type specie
                                                                            Gammabaculoviridae is Neodiprion lecontei nucle
                                                                            drovirus (NeleNPV).
                                      Occlusion
Virions                                                                       Only one member of the genus deltabaculovirus
                                        body
                                                                            sequenced to date. Culex nigripalpus nucleopolyhe
                                                           Granulovirus     (CuniNPV) infects mosquitoes, a member of the D
                                                              (GV)          produces both BV (containing F protein) and O
                                                                            matrix protein shows no apparent homology to po
    SNPV
                                                                            or granulin and may represent a new family of o
                                                                            proteins (Perera et al., 2006).
                                                                              Most baculoviruses are species- or genus-spec
                                                                            are named after the insect that they infect. A
Figure 1 Occluded virions. Baculovirus genera are based on the structures
of occluded virus, polyhedral shaped for nucleopolyhedrovirus (NPV) with
                                                                            exception to this rule is AcMNPV, which can infec
many enveloped nucleocapsids or smaller ovoid occlusions with a single      32 different lepidopteran insects from 12 families
nucleocapsid for granulovirus (GV). NPVs may contain multiple
nucleocapsids (MNPV) or single nucleocapsids (SNPV).                                             Guarino, 2011
Viral evolution, some economic approaches
Zombie / Gooey
Zombie / Gooey

                      egt    chit
                             cath




Hawtin et al, 1997
Hoover et al, 2011
Viral evolution, some economic approaches
Viral evolution, some economic approaches
Viral evolution, some economic approaches
Viral evolution, some economic approaches
Viral evolution, some economic approaches
Ecological
inheritance
                                                            EGT level




                                              Fitness
                                                        

                                                                0   2             3   T
                                                                                            




Viral generation
                                                                        X Axis




within host                     0                           1            2            ...                           T




                                                                                                Fitness
              Fitness




Genotype
fitness                 

                            zg Zg zG ZG
                                          
                                                               
                                                                                                              zg   Zg             zG   ZG
                                                                                                                                            



                                X Axis
                                                                                 X Axis
µ

Susceptible                Exposed           Carrier   Liquefied
                                         ⌫
                                                             ⌧
                   0
              L+       C
                                                   ✓    Reservoir




                                                                    ✏
⇣             0
                          ⌘⇣                    ⌘       ⇣             ⌘⇣         ⌘⇣                 ⌘
                                       ⌫                                    ⌫
R0 =        + +✓                      ⌫+µ           +        +⌧            ⌫+µ               + +✓




                                                µ

       Susceptible                    Exposed               Carrier          Liquefied
                                                    ⌫
                                                                                      ⌧
                              0
                         L+       C
                                                                  ✓              Reservoir




                                                                                             ✏
⇣             0
                          ⌘⇣                    ⌘       ⇣             ⌘⇣         ⌘⇣                 ⌘
                                       ⌫                                    ⌫
R0 =        + +✓                      ⌫+µ           +        +⌧            ⌫+µ               + +✓




                                                µ

       Susceptible                    Exposed               Carrier          Liquefied
                                                    ⌫
                                                                                      ⌧
                              0
                         L+       C
                                                                  ✓              Reservoir




                                                                                             ✏
Genotypes




            (z)ombie | (g)ooey
Genotypes




            (z)ombie | (g)ooey
niche
construction?
1.0
                         Susceptible

                         Exposed                        Whee!
                  0.8
% of population
                         Cadaver
                                                                                Sus.

                  0.6    Liquefied
                                                                                Exp.
                         Reservoir

                  0.4                                                           Cad.


                                                                                Liq.

                  0.2
                                                                                Res.


                  0.0                                                       t
                        20           40    60   80      100     120   140

                                          Time (days)
25




 20




 15
                                           Genotype
                                            zg




R0
                                            zG
                                            Zg
                                            ZG
 10




     5




     0

         0.0   0.2   0.4       0.6   0.8
                           γ
25




 20




 15
                                           Genotype
                                            zg




R0
                                            zG
                                            Zg
                                            ZG
 10




     5




     0

         0.0   0.2   0.4       0.6   0.8
                           γ
25




Fitness sequence:
                     20


zg < Zg < zG < ZG
                     15
                                                               Genotype
    =                                                           zg




                    R0
                                                                zG
                                                                Zg
                                                                ZG
                     10




                         5




                         0

                             0.0   0.2   0.4       0.6   0.8
                                               γ
0.5




0.4




                                Sequence
0.3                              No NC
                                 Zg,zG,zg
                                 zG,Zg,zg
θ                                Zg,zg,zG
                                 zG,zg,Zg
0.2                              zg,Zg,zG
                                 zg,zG,Zg



0.1




    0.5   1.0       1.5   2.0

                β
Culex nigripalpus NPV
       Neodiprion abietis NPV
       Neodiprion lecontii NPV
       Neodiprion sertifer NPV
       Pieris rapae GV
       Choristoneura occidentalis GV
       Clostera anachoreta GV
       Cryptophlebia leucotreta GV
       Cydia pomonella GV
       Adoxophyes orana GV
       Phthorimaea operculella GV
       Agrotis segetum GV
       Plutella xylostella GV
       Spodoptera litura GV
       Pseudaletia unipuncta GV
       Helicoverpa armigera GV
       Xestia c-nigrum GV
       Leucania separata NPV
       Spodoptera litura NPV
       Choristoneura fumiferana MNPV
       Orgyia pseudotsugata MNPV
       Hyphantria cunea NPV
       Antheraea pernyi NPV
       Epiphyas postvittana NPV
       Anticarsia gemmatalis NPV
       Choristoneura fumiferana DEF MNPV
       Maruca vitrata MNPV
       Bombyx mandarina NPV
       Bombyx mori NPV
       Plutella xylostella multiple NPV
       Rachiplusia ou MNPV
       Autographa californica NPV

egt    Lymantria xylina MNPV
       Lymantria dispar MNPV
       Helicoverpa armigera NPV NNg1

chit
       Helicoverpa zea SNPV
       Helicoverpa armigera NPV
       Helicoverpa armigera NPV G4
       Adoxophyes orana NPV

cath   Adoxophyes honmai NPV
       Clanis bilineata NPV virus
       Ecotropis obliqua NPV

null   Euproctis pseudoconspersa NPV
       Orgyia leucostigma NPV
       Trichoplusia ni SNPV
       Chrysodeixis chalcites NPV
       Helicoverpa armigera multiple NPV
       Mamestra configurata NPV-B
       Mamestra configurata NPV-A
       Agrotis ipsilon multiple NPV
       Agrotis segetum NPV
       Spodoptera frugiperda MNPV
       Spodoptera litura NPV II
       Spodoptera exigua MNPV
Granulovirus Morphs

Type I
•Infect only midgut and fat bodies.
•Kill slowly, little or no liquefaction.


                           Type II
                           •Infect multiple tissues.
                           •Kill more quickly, liquefy the host.
Pieris rapae GV



Zombie/Gooey              Choristoneura occidentalis GV


egt   chit                Clostera anachoreta GV


      cath                Cryptophlebia leucotreta GV



                          Cydia pomonella GV



                          Adoxophyes orana GV



                          Phthorimaea operculella GV



                          Agrotis segetum GV



                          Plutella xylostella GV



                          Spodoptera litura GV

         egt    Type I
         chit   Type II   Pseudaletia unipuncta GV

         cath
         null             Helicoverpa armigera GV



                          Xestia c-nigrum GV
Viruses are driving behaviour....
for their own benefit!
Viral evolution, some economic approaches
Viral evolution, some economic approaches
Viral evolution, some economic approaches
Viruses mutate quickly.
(Holmes, 2008)
                        6
                                                                                                                        Some RN
                                                                                                                        number
                                                                                                                        rates of
Genome size (log(Kb))

                        5                                                                                               of these
                                                                                                                        Phylogen
                                                                                                                        SFVs is l
                                                                                                                        This wid
                        4
                                                                                                                        tion to b
                                                                                                                        fossil rec
                                                                                                                        site/year
                        3                                                                                               among S
                            0        –1       –2        –3        –4        –5       –6        –7         –8       –9   indicatin
                                          Mutation rate (log(mutation per site per genome replication))                 mechani
                            +ssRNA        –ssRNA             Retro          dsRNA           dsDNA              ssDNA
                                                                                                                        likely exp
                                                                                                                        in SFV i
   Figure 1 | Average rates of spontaneous mutation in viruses, adjusted to the rate per                                primaril
   genome replication. Positive-sense single-stranded (ss) RNA viruses (+ssRNA; RNA phage
Viral evolution, some economic approaches
virus grows exponentially
growth rate, b




                               U
                     b = re
                 U
deleterious mutations are fatal




                                  advantageous mutations
                                  increase transmission (only)
bt                   Z       T                   ✓           b(1+ )(T   ⌧)
                                                                                      ◆
¯=   c(e             1)                                         (1 + s)(e
R                         +c                f (⌧ ; ↵U, b)
               b                    0                                 b(1 + )
         b(T    ⌧)
     e                    1
                              )d⌧
                b
Downloaded from rspb.royalsocietypublishing.org on Feb


                   Life history
                                                                                                        A determin
                      virulence threshold, D                     host dies                           with the follow
                                                                                                     dV
                                                                                                         ¼ ð1 À a Þð
                                                                                                                ^




                                                                        clearance by immune system
                                                                                                     dt
 log(viral load)                                         b*                                          dW
                                                                                                         ¼ ð1 À a Þd
                                                                                                                 ^
                                                                                                      dt
                                                                                                            À vW;
                                                                                                     dX          ^
                                                                                                        ¼ a ð1 À d Þ
                                                                                                          ^
                                                                                                     dt
                                                                                                          À vX;
                                                                                                     dY     ^ bu eÀ
                                     infection
                                                                                                        ¼ ad
                                                                                                          ^
                                                                                                     dt
                                     duration, T
                                                                                                            ^
                                                                                                          þ d ð1 þ
                                           time (t)
Figure 1. The relationship between virulence, clearance by the immune
                                                                                                           du
system and the duration of infection. Five examples of viral trajectories are                        and        ¼ Àb
What did we find?
3.0

                         –                                                                –
    2.5
      (a)          log10(R), constant infection duration       (b)                  log10(R) with virulence
            3.0
                        5
    2.0     2.5         4
r           2.0         3                                                           0.85
                                                                          grow quickly, accurately
    1.5            0.85                                                      0.75
      r            0.852                                                            0.85
            1.5     01
    1.0             −1                                                                    −1
            1.0                                                               1
                        0
    0.5            −2                                                        1.25
                                                                                          −2
            0.5       −1
                                                                             1.5

       −3     −3      −2
                       −2          −1
                                   −1           0   0      1         1
                                                                     −3      −3
                                                                              −2             −2
                                                                                             −1          0 −1
                                 log10(U)                                                               log10(U)
                            –                                                     –
3.0

                          –      –                                                         – 5
ation   2.5 (b)
          (a)              log10(R) with virulence
                    log10(R), constant infection duration       (b)                  log10(R) with virulence
              3.0




                                                                                             rspb.royalsocietypublishing.org
                       5
        2.0   2.5      4
  r           2.0      3                                                             0.85
                                                                           grow slowly, inaccurately
        1.5         0.85
                      0.75                                                    0.75
          r         0.85
                       2                                                             0.85
              1.5   01
        1.0         −1 1                                                                    −1
              1.0                                                              1
                       0
        0.5         −2
                     1.25                                                     1.25          −2
              0.5      −1




                                                                                             Proc R Soc B 280:
                       1.5                                                    1.5

          1 −3 −3      −2
                        −2           −1
                                    −1
                                    −1           0
                                                 0   0      1
                                                            1          1
                                                                      −3       −3
                                                                                −2                     −2
                                                                                                      −1                       0 −1
                                  log10(U)                                                                                     log10(U)
                           –
                           –                                                       –
−3        −2         −1         0           1         −3        −2         −1         0

                         –                                                     –
    2.5
      (c)          log10(R) with virulence and immunity       (d)        log10(R) with virulence and immunity
            3.0

    2.0     2.5

r           2.0                                                      intermediate 0.85
                                                                                   growth, mutation
    1.5            0.85
      r            0.85                                                    0.85
                                                                                     0.85
            1.5     00.85
    1.0              0.85
                    −10                                                    0.85
                                                                                      −1
            1.0       −1                                                    −1
    0.5            −2                                                                 −2
            0.5       −2                                                    −2


       −3     −3       −2
                        −2         −1
                                  −1          0   0       1         1
                                                                    −3      −3
                                                                             −2          −2
                                                                                        −1          0 −1
                                log (U)
                                log10(U)
                                    10
                                                                                      log10(U)     log10(U)
What does this tell us?
What does this tell us?
Viral evolution, some economic approaches
Viral evolution, some economic approaches
Viral evolution, some economic approaches
Thanks!



tanaka lab
Viral evolution, some economic approaches
Viral evolution, some economic approaches

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  • 5. ... “the phenomenon of constructing, destroying, or altering one’s environment and thus changing the selection pressures exerted by that environment.” Boni and Feldman, 2005
  • 6. Populations of t Et Natural selection Gene diverse pool phenotypes Genetic inheritance time Populations of Gene t+1 Et+1 Natural selection pool diverse phenotypes
  • 7. Niche construction Populations of t Et Natural selection Gene diverse pool phenotypes Ecological inheritance Genetic inheritance time Niche construction Populations of Gene t+1 Et+1 Natural selection pool diverse phenotypes
  • 8. Embioptera Synbranchiformes Sarcophagids Swallows Helicopsychidae Fungi Ptilonorhynchidae Mosses Uropeltidae Termites Birds Apodidae House martin Dipodidae Kingfishers Bees Milkweed Trochilidae Vombatidae Ophichthidae Alligators Cyanobacteria Chameleons Lampreys River otters Beavers Gastercantha Myrmeleontidae Gecko Hydropsychiade Amphibians Cassava Red admiral Testudinata Cyclosa Iguanas Lycosidae Rhynchocephalia Acacia Blattodea Pipesnakes Toadfish Myctophidae Chiromantis Worms Bathyergidae Crocodiles Sandpipers Apicotermes Lizards Ctenizidae Opossum Bombyliidae Testudinidae Merganser Siluriformes Wren Symphyta Drosophila Stomiiformes Smelts Turkeys Isopods Membracidae Black rush Beetles Psocoptera Mallos Marmots Euchondrus Cynomys Gasterosteus Tenebrionidae Pongidae Galliwasps Honey eater Rabbits Zebras Bembix Areneus Tuna Homo Ergot fungus Philopotamidae Crustaceans Flatworms Sphagnum Oviparous insects Finch Congridae Melinae Alcedinidae Hirundinidae Mammals Ant lions Snake eels Atta Vanessa Hamsters Sharks Parus Peromyscus Owls Scolytidae Parasitoid insects Cricitelus Galaxids Liphistiidae Eublepharidae Coniosporium Momotidae Muskrats Eider duck Hemiptera Algae Capitonidae Plants Buffalo grass Petrel Periophthalmus Uloborus Turdus Tuatara Teiidae Tephritid flies Paelobatidae Meropidae Lanternfishes Passalidae Badgers Sauria Chaparral Swifts Coral Mudskippers Gerbils Animalia Millipedes Grasses Moths Dolphins Snails Gryllotalpidae Vulpes Weeverfishes Ploceidae Malaria Ichneumonidae Batrachoididae Ensiferan Cormorants Scombridae Tortoise Tachyoryctes Macronema Theridion Mosquitoes Dragonfishes Wombats Spalax Hornbills Typhlopidae DiatomsLichens Snakes Bowerbirds Mole rats Deinopidae Ostariophysi Rooks Caecilians Bucerotidae Pleurodira Macrotermitinae Microhylidae Rodents Pisauridae Catfish Prairie dogs Jerboas Puffinus Scarabaeidae Cows Moles Anguillidae Cyclorana Paradise fish Carp Limnephilidae Rats Salmon Coleoptera Thrush Protists Pythons Cattle Frogs Eucalyptus Argyroneta Caelifera Flies Wasps Tits Lobsters Snapping shrimps Reithrodontomys Turtles Cuckoo Squirrels Earwigs HedgehogsKatydids Guinea pigs Osmeridae Hirundines Magpies Lutra Dibamids Lepidoptera Eels Chiroptera Trachinoidei Ovenbirds Lovebirds Louse Neanderthals Bats Cichlids Viruses Agapornis Caterpillars Porcupines Erinaceus Amphipods Reptiles Trionychidae Gazelles Mites Vertebrates Characiformes Gymnopphiona Eumenidae Barbets Bark lice Voles Primates Beeflies Cavia Trichoptera Silverfish VespinaeFishes Dipterans Whales Cicadas Wildebeest Weaverbirds Cod Trees Braunsapis Bacteria Helodermatidae Polistinae Braconidae Archaebacteria Chough Beech trees Leptotyphlopidae Microphytes Petromyzontiformes Hemisotidae Terrapins Foxes Eubacteria Spiders Guppies Megapodes Aniliidae Amphisbaenia Vipes Picidae Locusts Tapinillus Basidiomycetes Furnariidae Storks Viceroy Teleutomyrmex Insects Scincidae Thysanoptera Treehoppers Corvids Acrididae Eagles Zooplankton Clupeiformes Mouthbrooder Monarch butterfly Tetragnatha Hominids Skinks Orthoptera Segestria Pine trees Gophers Apinae Arachnids Dendrobatidae Dermaptera Segestriidae Sawflies Grasshoppers Flowering plants Pygopodids Motmots Hystrix Butterflies Lemmings Nile monitor Bee eaters Sardines Epiphytes Hummingbirds Ariadna Gobies Rhinophrynidae Anomalepididae Painted lady Ants Stickelback Woodpeckers Sea turtle Hymenoptera
  • 9. histiidae Eublepharidae Coniosporium Momotidae Muskrats Eider duck Hemiptera Plants Turdus Tuatara Teiidae E Petrel Periophthalmus Uloborus Tephritid flies Pa pidae Chaparral Swifts Lanternfishes Passalidae A asses Moths Coral Mudskippers Gerbils Vu ceidae MalariaDolphins Snails BatrachoididaeIchneumonidae Gryllotalpidae Cormorants Scombridae Tortoise Theridion Mosquitoes Dragonfishes Ensiferan Wombats Spalax Hornbills Typhlopidae Lichens Mole rats Deinopidae Ostariophysi Rooks ae Pisauridae Macrotermitinae Microhyl Rodents Catfish Prairie dogs Jerboas uffinus Pleurodira Moles AnguillidaeRats Cyclorana Paradise fish Carp Salmon Coleoptera Thrush Protists Pythons Cattle Frog Eucalyptus Wasps Tits Snapping shrimps Reithrodontomys Turtles Diatoms rrels Earwigs Hedgehogs Katydids Guinea pigs Osmeridae Hirundines Magpies Lutra Dibamids Lepidoptera Eels Chiroptera ebirds Louse Neanderthals Bats Cichlids Viruses Caterpillars Agapornis Porcupines pods menidae Reptiles Trionychidae Gazelles Mites Bark lice Characiformes Voles Primates Beeflies Barbets Cavia Trichoptera Fishes VespinaeDipterans Whales icadas Wildebeest Weaverbirds Cod Silverfish Bacteria Helodermatidae Polistinae Braconidae Chough Beech trees Leptotyphlopidae Microphytes omyzontiformes Eubacteria Foxes Guppies Megapodes Aniliidae Amphisbaenia Vipes Locusts Tapinillus Basidiomycetes Viceroy Teleutomyrmex ts a Treehoppers Corvids Acrididae Zooplankton Clupeiformes
  • 13. Why manipulate the host so dramatically? How do such manipulations arise? How do niche effects outside the host affect the virus?
  • 15. Baculoviruses Nucleopolyhedrovirus the point where they are unrecognisable or whe (NPV) have lost the genes entirely. There is some data to MNPV that the hymenopteran viruses may not spread be midgut, in which case a budded virus (BV) form m necessary (Duffy et al., 2006). The type specie Gammabaculoviridae is Neodiprion lecontei nucle drovirus (NeleNPV). Occlusion Virions Only one member of the genus deltabaculovirus body sequenced to date. Culex nigripalpus nucleopolyhe Granulovirus (CuniNPV) infects mosquitoes, a member of the D (GV) produces both BV (containing F protein) and O matrix protein shows no apparent homology to po SNPV or granulin and may represent a new family of o proteins (Perera et al., 2006). Most baculoviruses are species- or genus-spec are named after the insect that they infect. A Figure 1 Occluded virions. Baculovirus genera are based on the structures of occluded virus, polyhedral shaped for nucleopolyhedrovirus (NPV) with exception to this rule is AcMNPV, which can infec many enveloped nucleocapsids or smaller ovoid occlusions with a single 32 different lepidopteran insects from 12 families nucleocapsid for granulovirus (GV). NPVs may contain multiple nucleocapsids (MNPV) or single nucleocapsids (SNPV). Guarino, 2011
  • 18. Zombie / Gooey egt chit cath Hawtin et al, 1997 Hoover et al, 2011
  • 24. Ecological inheritance EGT level Fitness 0 2 3 T Viral generation X Axis within host 0 1 2 ... T Fitness Fitness Genotype fitness zg Zg zG ZG zg Zg zG ZG X Axis X Axis
  • 25. µ Susceptible Exposed Carrier Liquefied ⌫ ⌧ 0 L+ C ✓ Reservoir ✏
  • 26. 0 ⌘⇣ ⌘ ⇣ ⌘⇣ ⌘⇣ ⌘ ⌫ ⌫ R0 = + +✓ ⌫+µ + +⌧ ⌫+µ + +✓ µ Susceptible Exposed Carrier Liquefied ⌫ ⌧ 0 L+ C ✓ Reservoir ✏
  • 27. 0 ⌘⇣ ⌘ ⇣ ⌘⇣ ⌘⇣ ⌘ ⌫ ⌫ R0 = + +✓ ⌫+µ + +⌧ ⌫+µ + +✓ µ Susceptible Exposed Carrier Liquefied ⌫ ⌧ 0 L+ C ✓ Reservoir ✏
  • 28. Genotypes (z)ombie | (g)ooey
  • 29. Genotypes (z)ombie | (g)ooey
  • 31. 1.0 Susceptible Exposed Whee! 0.8 % of population Cadaver Sus. 0.6 Liquefied Exp. Reservoir 0.4 Cad. Liq. 0.2 Res. 0.0 t 20 40 60 80 100 120 140 Time (days)
  • 32. 25 20 15 Genotype zg R0 zG Zg ZG 10 5 0 0.0 0.2 0.4 0.6 0.8 γ
  • 33. 25 20 15 Genotype zg R0 zG Zg ZG 10 5 0 0.0 0.2 0.4 0.6 0.8 γ
  • 34. 25 Fitness sequence: 20 zg < Zg < zG < ZG 15 Genotype = zg R0 zG Zg ZG 10 5 0 0.0 0.2 0.4 0.6 0.8 γ
  • 35. 0.5 0.4 Sequence 0.3 No NC Zg,zG,zg zG,Zg,zg θ Zg,zg,zG zG,zg,Zg 0.2 zg,Zg,zG zg,zG,Zg 0.1 0.5 1.0 1.5 2.0 β
  • 36. Culex nigripalpus NPV Neodiprion abietis NPV Neodiprion lecontii NPV Neodiprion sertifer NPV Pieris rapae GV Choristoneura occidentalis GV Clostera anachoreta GV Cryptophlebia leucotreta GV Cydia pomonella GV Adoxophyes orana GV Phthorimaea operculella GV Agrotis segetum GV Plutella xylostella GV Spodoptera litura GV Pseudaletia unipuncta GV Helicoverpa armigera GV Xestia c-nigrum GV Leucania separata NPV Spodoptera litura NPV Choristoneura fumiferana MNPV Orgyia pseudotsugata MNPV Hyphantria cunea NPV Antheraea pernyi NPV Epiphyas postvittana NPV Anticarsia gemmatalis NPV Choristoneura fumiferana DEF MNPV Maruca vitrata MNPV Bombyx mandarina NPV Bombyx mori NPV Plutella xylostella multiple NPV Rachiplusia ou MNPV Autographa californica NPV egt Lymantria xylina MNPV Lymantria dispar MNPV Helicoverpa armigera NPV NNg1 chit Helicoverpa zea SNPV Helicoverpa armigera NPV Helicoverpa armigera NPV G4 Adoxophyes orana NPV cath Adoxophyes honmai NPV Clanis bilineata NPV virus Ecotropis obliqua NPV null Euproctis pseudoconspersa NPV Orgyia leucostigma NPV Trichoplusia ni SNPV Chrysodeixis chalcites NPV Helicoverpa armigera multiple NPV Mamestra configurata NPV-B Mamestra configurata NPV-A Agrotis ipsilon multiple NPV Agrotis segetum NPV Spodoptera frugiperda MNPV Spodoptera litura NPV II Spodoptera exigua MNPV
  • 37. Granulovirus Morphs Type I •Infect only midgut and fat bodies. •Kill slowly, little or no liquefaction. Type II •Infect multiple tissues. •Kill more quickly, liquefy the host.
  • 38. Pieris rapae GV Zombie/Gooey Choristoneura occidentalis GV egt chit Clostera anachoreta GV cath Cryptophlebia leucotreta GV Cydia pomonella GV Adoxophyes orana GV Phthorimaea operculella GV Agrotis segetum GV Plutella xylostella GV Spodoptera litura GV egt Type I chit Type II Pseudaletia unipuncta GV cath null Helicoverpa armigera GV Xestia c-nigrum GV
  • 39. Viruses are driving behaviour.... for their own benefit!
  • 44. (Holmes, 2008) 6 Some RN number rates of Genome size (log(Kb)) 5 of these Phylogen SFVs is l This wid 4 tion to b fossil rec site/year 3 among S 0 –1 –2 –3 –4 –5 –6 –7 –8 –9 indicatin Mutation rate (log(mutation per site per genome replication)) mechani +ssRNA –ssRNA Retro dsRNA dsDNA ssDNA likely exp in SFV i Figure 1 | Average rates of spontaneous mutation in viruses, adjusted to the rate per primaril genome replication. Positive-sense single-stranded (ss) RNA viruses (+ssRNA; RNA phage
  • 46. virus grows exponentially growth rate, b U b = re U
  • 47. deleterious mutations are fatal advantageous mutations increase transmission (only)
  • 48. bt Z T ✓ b(1+ )(T ⌧) ◆ ¯= c(e 1) (1 + s)(e R +c f (⌧ ; ↵U, b) b 0 b(1 + ) b(T ⌧) e 1 )d⌧ b
  • 49. Downloaded from rspb.royalsocietypublishing.org on Feb Life history A determin virulence threshold, D host dies with the follow dV ¼ ð1 À a Þð ^ clearance by immune system dt log(viral load) b* dW ¼ ð1 À a Þd ^ dt À vW; dX ^ ¼ a ð1 À d Þ ^ dt À vX; dY ^ bu eÀ infection ¼ ad ^ dt duration, T ^ þ d ð1 þ time (t) Figure 1. The relationship between virulence, clearance by the immune du system and the duration of infection. Five examples of viral trajectories are and ¼ Àb
  • 50. What did we find?
  • 51. 3.0 – – 2.5 (a) log10(R), constant infection duration (b) log10(R) with virulence 3.0 5 2.0 2.5 4 r 2.0 3 0.85 grow quickly, accurately 1.5 0.85 0.75 r 0.852 0.85 1.5 01 1.0 −1 −1 1.0 1 0 0.5 −2 1.25 −2 0.5 −1 1.5 −3 −3 −2 −2 −1 −1 0 0 1 1 −3 −3 −2 −2 −1 0 −1 log10(U) log10(U) – –
  • 52. 3.0 – – – 5 ation 2.5 (b) (a) log10(R) with virulence log10(R), constant infection duration (b) log10(R) with virulence 3.0 rspb.royalsocietypublishing.org 5 2.0 2.5 4 r 2.0 3 0.85 grow slowly, inaccurately 1.5 0.85 0.75 0.75 r 0.85 2 0.85 1.5 01 1.0 −1 1 −1 1.0 1 0 0.5 −2 1.25 1.25 −2 0.5 −1 Proc R Soc B 280: 1.5 1.5 1 −3 −3 −2 −2 −1 −1 −1 0 0 0 1 1 1 −3 −3 −2 −2 −1 0 −1 log10(U) log10(U) – – –
  • 53. −3 −2 −1 0 1 −3 −2 −1 0 – – 2.5 (c) log10(R) with virulence and immunity (d) log10(R) with virulence and immunity 3.0 2.0 2.5 r 2.0 intermediate 0.85 growth, mutation 1.5 0.85 r 0.85 0.85 0.85 1.5 00.85 1.0 0.85 −10 0.85 −1 1.0 −1 −1 0.5 −2 −2 0.5 −2 −2 −3 −3 −2 −2 −1 −1 0 0 1 1 −3 −3 −2 −2 −1 0 −1 log (U) log10(U) 10 log10(U) log10(U)
  • 54. What does this tell us?
  • 55. What does this tell us?