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The classification of organisms at the edge of life, or problems with virus systematics

182
\ttnzl. Ra,rc ol bmita
d.i*dlodt.6|'!E4Rkdimal*r'Jl
o'4"8ni4. PhD ft.n. !iit6n' of N.r.t,
e. cLrr F.4.. cdi R.M. ed MniT.R.09r:,.
r.ir ni:hB. ,'. ,'rrr &r- 2t. .1r-4.
r0. Du&.b. o. (ret. 7 .,teodaltr@,.", n
l^.d.'nBiod.bM^idE.,dry|.n.'Ms.
(Aadc.)
ft6n, U.ivdiry or N.d, Pi.idffirirz
ff,8udh.h D.r.
(rer7).
Souh Aln antonnat olScie$. vol.86 Aprit I99o
iroradr i' tat'.ti.*.e Msc ( aic.) rh6ir,
Univairy or Ntd, Piamrrirblll.
rr_ cfl3 R.M., Filr'd c. rn &..dbar r.^. o9r.).
w@!dt Pdh4 c6@, *.tl - ?lr_ Hdanri.
rr, Edhur c.c. &d Fsh( c. (1916).
Pftbrtu in
truln'ionrl thFry' ln,*le'l i1'q4''a6 o/
PNtnt Md Nndnortl Re.h, dir c.E d
1.. cd! R-M.
(1946)-
Mou@ar or apoe id
Iulni.i.lqFind!'|iN,.n!..f,4!''a6
.l Ptutt! ed N&nioat zern. .dit. c_ Ftll5
''ld.'9^N's'||9|','A^.'pr8d|toddliQ
l.d hbt., bd, .aivotine ud ,utur n.
4r'z'd6 r ,r,," ,t . Ms. t^si..) rh6n,
univ.riry of N.r.l, Pnr.m.dkbu4.
16. lndaodl M,M.v. (
lele). c,'oial.d''4 ir 3D,-
i,t r/r' Msc
(^eic.)
rh6n. uniEBny or Naur,
The classification of organisms
at the edge of life
or Problems with virus systematics
EdwardRybicki
vlruldrndcl.tslnedon
Probl.nlr eirh thc claifi@tion of
viru*s st..t.d wifi ftei. disdery nca.
rh cnd of thc lasr centu.y, dd have
co inucd wr sin@. E.dy p@bloc wr
concncd *ith jllsl wh.t viNs wcrc: n
is only sincc uc 1950s
- *ith fie ldvnt
ol molccular biology
- thrr they could b.
slrisfacrorily dcfincd. Vidss are noq
ro$iscd as bc'.8 pototially ?atho-
gcnjc, obligately intrrcclluld pdasitsr
wnh gcnomB
coBisting oi eirber DNA o.
RNA, which rcplicare icide hosr celh in
rhc fofr ol theii
tamic nucleic eid:
which
G. h6t ccll mrchinat to syn-
thesia spccialisdl self-aembled pu-
ticl6 ellcd vi.i6, whos functim is lo
cdrrin lhc gcoomc
md rspon n f6fr
Alrhouth dirqfit braches ol violoty
di8in.llycvolrcddiff@ mdtrla$ral
ed t|ionoinic aylteN cording ro lhcir
paniculd bia6, sirce 1966 thc Imda-
tiall CotMjlte m T.xon@y of ViN-
cr (lCTv) hd ben rsponsiblc for rcsu-
latinS Lhc clasilication dd nommdaluc
of
viuscs.
This body is a cmnroe ol lh.
htcmatiof,ll Uf,ion of Mic.obiolocical
s@ictics
(ruM9. Ir has sub'comnrq
tor plmt.
uimrldd b&rc.ial
viNs,,nd
r coh@ body oi rulcs hd bcs cs-
llblishcd.r' South Africa hd eue eed
rcpNot.rion on this body a @h
naddal MicrcbioloSy Seicry lhar h4 d
activc intftst ir vircloty en nmiratc r
renbcn in ddnio, meBb6 my b.
nominaled fd th. eb<omtues.
Even
wilh thc ICTV, hoeever, clasifi
ciion of virus6 is by no trEd )r d
cx.cr ri6c.i n is aho to eft erlmr sill
caughr up
in
.r8m.nt!.orcdins tlE.c'
coSnirim ard .Min8 of di(I*nr rdom-
mic l./.13, or t.rc . Of,e of th
probl.m
helc i3 *h.th.r d not viruss sh@ld b.
cla!3ificd lik orh.r 6goisN: th is,
irto a hidlrchicll uructur. of speia aid
gercr!, ruilia, ribs a.d s olr arclhcr
is whcther
or Dor $c clNical Li@qn
sysrd of l.rinatc bindills should b.
ucd fd vir@1 Prcdict.bly, aridal .rd
espccidly humr! viruss h!v. bq!
mmd ,nd cl.ssilicd reddins to clNi'
ql idca: th.t ;s, with lins designated
a speics. .nd o.g.ni5cd inro
8.F4 $b-
rdiliB ed tailiBi with th6. raG
b.ing cffetircly htinis.d in that
gdric
t).m! c'rd in '-virus', sub-tmily mru
cDd in '-viriE.'. and fmilv ros in
'-vkid&'J' Fd crlrnple, titerc is rhc
fmil,! Papovarinddr, Be s Papilotu-
vir6, and sp@ics hms papillomvirus
tnc l6.r
Plet vkolosist5dc
mdd of akoserhq
morc c@trdy stutl: thcy have Golutely
aistcd ftc cncrorchnc.$
of Lllinl|c !o-
mcrlaturc aid Limen clNific.tion,
od hrvc contcnrcd thcmselves wnh collo
qlial Mmcs for p.nicul{ viruses
(equi'
valent lo thc spei.s levcll dd Dams
dcrivcd fiom hc t)?c rElnbd d flm a
gFup dcsiprid. fd Sdplevel
(@shly Bdu!-ldcl) idnifi@rid:
Thus. w. h.vc trom /'tdic, co*?ea
chlo.otic Eot|l. .nd b@d beo mrrl.
viru*s a $e tumbds of thc a.otu'
virus grorp. Planr
virclogisrs
do trd yct
re%nisc lny hi8her-levcl
tda fd purcly
plant
viruscs, alhough
discu$iotris
undd
w!y. Ot cousc, ehcrc virusBcrcs king-
dom bounddies, so da nomerclatue
@d chsincarionr fius, lhe diiferdt virus
fdrilies
Rhahjovindae
(c.r.
rabics
virus)
ed Reoviridae
(c.8.
rot.viN, soDe oi
which causc infantile dianho!) botl1
includc sev@l pllnt virc6, ehich are
inrcgFlcd iDro satially dimal virus
It app..rs obvio'! thlt 'h vit@s iD
@h fanily h0e . commdt volutidary
6igi.. dcspnc lhe rery diffde hosls
they
infccti Much vork has .qdy ben
don. m Scnmic squcrcinS oi vitus
inlecdng .ll rl?es of ortd's6, a.d rcla
tionship dcndroSr.,tls lnd phylose!.tic
EG bascd on squcllce analys.s
{e s|zn-
in8 ro b dd*,ll up for many 8roups
of
viru$s. Evolution!ry and bioseosraphic
speculadons n bcing made
ei$ i!o.s-
ins resuleiry, csp..ially for vi.uses in-
pondl ro h6s like influftzao ard
dcntuc fcvcr virus.? I h also irdes,
ilgly populq lo ue *qu6ce cmpan-
sm md phyloScndic aaly$s ror thc
cldsification ol dcfincd grolps ol plmr
And hcrcin lics . prcblm: should
th.
clasifietim of viruscs ctrrpt to rcnet
lhcn pbbablc phylog.iy, a is ofta th.
ce thcs d.ys eilh pldr 6d din.l
slstmtic!? Sholld vitllg h. grdpd
eodiry to lh.ir crcluionaly reladon'
ship! - r! rll!.cd by DNA or RNA q
protcin s.qudcc hmloti4, pqhaps -
instcad or or a! eell .s on physicll
prcpnics
such a! nuclcic scid
contdr a.d
lyp., norpholoSy and sology? li is vcry
Dr Edvql Rybicb n in 6c D.p{th-t ot
Mi@bioloay, Unitdiry of c:pc Toh,
Ron !.bo!dl. 7?00
Sold Afria
Biologitlt hov. o pto@ue.d kAdzrct to Mn4 clatsih a^.1 o,.l.t thcit ots^isN of
i,t.r.sl: this cornpubio^ h4 b2.^ di8^ilied by colli^t it tu^o6! o. tst Mtict. 'td
hos .wlee.l i^to d tci.rc. alt oJ its Nn. Thzt. a.. oft.n eiol.nt disagreetunts 6 to
asieM.^ts oI o,8a^is6, hMvel, which hae. ofi.^ b.e^ ftsohat 6 tuh bt Jot.e ol
pe.sonaliry 6 b, tse ol qu,tifabtedata. M@h har olto b.en wtitt.^ rcce^ , on th.
nlotivc nenB o! th. 6. oI @rpholosicat ud bioch.^icd cnkria lor bioloSical
ctAsi.licatio^ Gee crod lor d rcriew): thz qpticdtion ol tut crtat biolosicat
b.l^olo8! to sJst.Mtics is sti in its i^la"cti h.waet, tlEt. is nrch pto^ite i" itt
pole^tial lot B.utdlio^ oJ e6t a@u^ts oI ddtd lot th. prrcis. dnd aequiwcdl
clasificatio^olote6is^.Thz ain oJ this papt k to illatxat.tht act@l aMt potentia!
opplication of phllo8.n tic 4id other a@lts.t o! nrcLic dcid ard ptot.in s.qvEes of
iu.s to the t@rc6t ard ststeMtics oJ viws dnd, b! at.Nio^, b all oth2r
SuidAJhtaa|.Trd:*alenw.k^ttap vol.86 Aphl1aa0
DNI;\"i'J
lE3
viruses havc singl.{trddd RNA smo-
mes oi mund l0 0OO nucleotides h sie,
with a covalotly ltlached viss{odcd
proti! at
lhc 5 6d, od 3'-poly-A rajls
(like eukaryodc !RNAS). The Senone
may bc 'Ead ty hosr nbosones d{arly
upon 6lry ro rhe cell ro Prodee @ ldSe
'polt?6teh' which is fr@sed into
sevdal salld proreins, including {
viru{p@ific RNA depodent RNA poly-
mere or replic6., ud lhe fow coat d
capsid prcreid. The vitues als ploduce
ar le6l lwo speific lro(eas whjch @
rcspmible fd lhe prcesing of the
polnrotcif,. The genome replicats by
ryrlhcais upon dF gomic lemplatc of a
full-length compldmrary RNA; trris
rcnains ass@ilred i! a nenbrane-bound
rellicative complex that produces both
full lsgth gmomic and complementary
RNA. Tbe vnus replicde ha very lntle
sinilariry ro oy lrown hos!{oded en
zym.rt Tbc curendy acccptcn cbsifi-
cation of rhe viruses is inro four genqa -
0le Enrero', Aphrlc, Rbino' ed C&dio
viruses - ard a nmbd of unsrouped
virusesr
rhis clasificarim is ldscly bed
on physical p.opeflie of virions and
seroloEy, and panly on diseasc maniies
Th Catuvirus group - nmed for
co*pea hosaic virus (cpMv), lhe r}?e
member
- havc isomcuic
pdticlcs, twc
compon nt ssRNA gfloms (the lusq ot
which cd replicate independently of the
othq), only two coat protei6, od orly
(6 fd 6 is known) i.fect pl6rs. At fitst
sight, ftese vitusd apped distnc! frcm
lhe picoftavirues in eve.al impoflet
(=noTholosical) chalacreristics.
Hoe-
ever, they rcsemble pico.navitu*s in thrt
they have 5''gmome'linked p.oreins
(Vp t 6d poly A tails on each
gcnome
componenti tlD slme rddaional sEa
tegy a picm.viruses (proEolydc
cleavage of polFrotin); $e sde effec'
tive goc ordcr, dd dcrtable *qucncc
simil{.iris a! the mino acid level. In
oftn words, tney renble nothing n@
d les than r picomaviru which ha had
its senome dividd into capsid{elatcd od
replication-.elaled
segmenrs,
with the d-
dirion of a prorein for moveftenr in plants
at the
5' md of $ snallerM RNA" (*e
Fls. ?). Mo!@vq, it has bee! spculatcd
lhar picoma- ad Comovirus she a
spccific lcplic.tioo mechuism iNolvif,t
the us of a prorein (the 5' Vps) to
'prime' RNA synbesis up@ ! vi.al RNA
tcmptar.rl Ir on dsdq rhat cone
vioss des@ded flm a picomavitu-
Iike ucestd, Lhen rhc pr*ence of two
(and nor tl@) capsid pro(ei6 can be
oxplaincd
by usumina ftat the largcr
of
the two Comovirus plotcins is cit.']q a
Prodrcr of fusion of rhe vP2 and vPl
F.,i{,\
/\ I,\
I
Fi8. l. Du$dim of lnc difeM yps
of vtal Sqomic nucleic cids. TrE spcci6 d rhe
lmini of |lle @*s d rne
be of th. figuE rcpEst rhe bdic t}?es of gqooe of diffftnl
viruss. Ftr in(re, all dsRNA yirss hzy. lilrtr $gnot d gdom.q $DNA guodcs
@ be cimlr or 1i.6, sd iI cnolu, cu be singlc- or mulnsFponst. Cia. = circular
e8m. =
egmm..d: sinStc
= monopdi@.
tmpting ro say 'Yes! , and rush or to re-
define all the divisions berwen viruss
dd sroups of vituses. However, l]1* e
two main problms with $is approach
which dc fundamcntal ro 'he naru.c
of
viruscs, Oat m.y complicatc thc issue
Virusesandevolution
Tl'c finl major problcm is thar viruscs
{c, in all probability, polyphyletic in
origin - Lhat is. sevcral major groups of
viru*s arce by sevdal diiieror outes,
indepadmr ol each other, at differht
rimcs,-af,d have eprarc evoluriorary
his-
tdies.' ThB, it would be imposibl to
have . 'virus cvolurionry k@ , with m
Ur virus
ar rhc bsc blechinS nearly into
all of the modcm categdiesi nore likcly
fierc would havc ro bc scvqal Ees, ot
ditteror ages, sircs and compleiities.
Tlus, trclo should bc *vc.al distinct
clasificatm ehemes for virues, !cn@t-
ing fie b6ic Scnetic
divesny dd diiier
cn' oriBins. Fisurc 1 illGtrates sode of
thjs diveBity: in addnid to $e rdge of
t}?q is a rd8 in geromc size from rhc
>200000 neleotides of $e doubl
srrdded DNA poxviru$s ro rhe -5000
nucleotids oi somc +ssRNA
viruscs.
It
contrast, modem celhlar or8eisms -
prok.ryorc or cukaryotc - havc genomes
coBisting of double{rddcd DNA o4t;
this is cither prcdomineLly cncuh ard
sinsle{omporent (pokaryors) or linear
ed nulri{mpone (cukar}otes)
- al-
togelhs fu sidpler, and probably of fe
ftc *cond na.jor problm in con
sidci.E th higherlevcl clGsificatid of
viruscs irvolvs l:he
very naurc ol viruses
s i.depndmLly.cplicating dgmisms
To cxplain lhis. it is 6rst ncccss{y ro
dcscnbc
'n
dc[il fic genonic organiza-
lion - as revealed by nucleic eid se-
quencing
- of. fcw of lhe simplerviru-
ca, and rhcn ro explain how fte componsr
pans relare to rho* of othd viru*s. For
lhc sakc of simplicny I BillcoNidcr only
+ssRNA vitues fron a few fmilies:
however, the p.incipis outlincd ed thc
conclsios reachcd havc wide applica-
tion
in this
fiald. I hopc als lo show ho*
coGidelarion ot sequcnce dam may prc
fourdly chansc acccpicd cldsilicalion
$hedes, both fd vitws dd celluld
or8misrns. Fo. the pu.po$i of r'ris rcviev
I have ucd mino acid ejuoce 4lisn-
ments and tlE PRoPARS progrm lrom
the PC vesion ot PHYLIP (phylogeny
inferen@
pekage) vesion 3.1 of J. Fel
scnstcin
(Depryuncnt
oi Ccn.rics, Univer-
siry oi Seaulc) iq cladistic anatyss.
Aligmcnts oi nuclcic acid scqumcs, or
distarce dara, or orher compuler
proBram
may
also obviously bc
Ncd.
The Picorna.likevkussuprfamily
Pi.omaviNd (iamily Picomavi.idae)
e dongsr lhe sinpld vires they have
very sall, rcladvly simple, non<nve
loped isodric pqticlcs, consisting of
$rce or iolr diffe.ent proreins. True
picomaviruses @ bsr known frod lhe
flimal kingdom: *ell-krown repr*nia-
tivcs i.clude polionychis virus, i@L
dd mouh diseas virus,
and fie comon
cold-causing eenus ot lhinoviruses-r
However, there is also a Srowin! !@be!
oi iisr pi@ft{viruss o. picmalike
viruses,
and r@tly two ditfrcnt plot
picmalikevirus hav. bd d*dibed.'
ftcliminry obsedatids by ouwlvs
dd othc6 uc thlt pi@ma'like virus oi
i@crs diffd mde lh& picomviruscs of
mamds, indicdins dar ficso viruss
d.y have oriBinarcd in irsccts.lo Thc
184 SouthAiica^louArtoIS.i.^.. Vot.86 Ap,it19N
cally edg.d protcin
subuniB of I singlc
ryPc co{ing I sinSlco(poEor lG
hlob.lc irRNA gcno.nc
- which ha r
5 -Vpg &d | 31poly-A lail. This d bc
tularcd to Sivc . pol)?btci. ir dtBr
ci..dy thc r!m. way a Coo- .td
picornavirusd, with the santc 'cor.
ft .mbranc-bindinS prctin-prolc.sc-poly-
Fq4* (Mcn-Pror-Pol) ss. oldcr (s.,
Fis. 2), .!d F6umably rhc s.ft rcpli-
cltion nechartsd! Thc Potyvirulca dso
h.rc a VPt g4 in th. s'c rchdrc
posirio! .s in Oc pic@- ud Co6o-
vilEs. Wlat b morc, sisnificut simil.'
.iris in dcdu@d Mino acid squcrE.
a.
appd6r or cooparison ot thc pur.dvc
polr?oEin lcqercd of Poty-, Como-
ed piccnrvirus.s, 6pei.Iy ir th.
Esi6 of th. suppo$d rcpri@ aE)m.
lnd pro.ce .cqu@$" A ujor
diff.M@ b.rw@ Poty- ard picoin.-
vilws. howdd. is lh absdcc of coar
prctein(s) ar lhc NH?- tminu! of he
polnroEin
in Potlairu*s:
fi. singl. coat
pbtein Scoc' h iBlcad pe6r { thc
COOH- terminus, od is snuctually and
fwtiotully more simild lo th. prot is
fdld ir virus with todlik p.nicler
s@h s rcb.cco mos.ic virc th'll n is ro
ey virus wirh ism.Eic cap3ids.r A
similriry bclwcctr Poty- ald Comovirun
B is tbat ! 8nc
for ftoveme mplmBis
Fcst !r thc NHr- teninus of rhc
polt?rcrcini rhc PotFirus p!or.in, how-
qq, is 8or. similrt to tlE dc pcgscd
by iob@o m6dc viru thd il i! to &.
@ of CPMV. Thc 'h.lp.r compolctri
proEin
of TVMV - Espmiblc for .phid
tresission - hls no cquivalcnt i! thc
oth.r virulcs, but h sinilar to tic orc
found in thc uruelatd
DNAentainini
bmcuic Crulitrtovirus g!oup.'r Thi;
.PP.!anr mixrur! of fclnl.es of oh6
vins.s prolrptcd Urc Dutch nolccul.t
viroloeGt, Rob Ooldbtc.h, [o rcfd lo
Potyvilusc! |l'lhc oklpi dagst dE
viru*s'.r! Howcvcr, ftc .ppamdy
otud.d 'coro' .l.ftnt ot a mmbrurc-
binding protcin-protc.s.-lolymcrus. i3
thc stongcn fanlre of sinihtity b.twc.n
Potyviruscs rnd thc Comovirus
Iroup ad
TVIVV
B
CplvlV
M
pror.... pory6.r'3a co.i 0.or
\
Fs. Z Codpcisn of d. pFrqin coding cgion. of oic goona ol Plmvirues, Coho-
vitus Md Porlaitus. DincF.Ll, !h.d.d bor.r Eptlqt (ro tc!.) trE gd* @dcd fo. in
rhc
gftnic RNAr ol th.6wFr modc ComwiNr (CpMv:
t*o RNAS, B a'd M). dc
bb..6 tcin moulin8 Poryvirur
(IvMv), &d rlE polimtc!$ pim.vidi Th! g@ t!.c.
dc G gjs qlEE E & ldbh vPl - 4: c+ti pd.is in poliovitu: CPI - 2:
c+.id plud in CpMv: vrc: ldnc.li{tlcd plotcini m6. Uldi.e d m.mh urd:
nHhr&.hidi.8 Fd.nq mrc.d Fd: p@ir sFd!.d wid m@cIE. i, tldsi
lr.lF @hFd: .Prnd .r$8inio fdori ?: pddt' of unb.m fe'cin g.rch.d
r!gi@ bcsa 0E gsbB cprqdr drdl,r pddn r.qffia d (brict h.ddn8)
qrdudly Eldql Fd.is. At@r rM dE TvMv 8tu6c idir. .q!aE d tscuad
nnil'ny wilh pFki$ of dna viDr 8@ps, Th. d.gm ,a drh non infm.rim
obr.iftd frem Eft | 0, 11. | 2 &d 15.
gcB of picomvi|1ls,lr d ft.t ftc Yd &othcr plrnt viru gdp (th.
picmavnrl Foi.ic twlt ft@ clqv.g Potaiins 8too9, mdt d fd por.to virllt r.
of a rwedomin cl)mvidlik! gcE. PvY) which rr fi6t sigbt bcr'3 no
Onc may .xplain thc addcd ulovmefl lehtio hip whaEdd to .ithd Colr|o-
FoL.in tcnc by invobnt RNA rccombi- or p'cornlviru*s, ir als .ppscndy r
nari6, which i3 kroq ro Gcur for a o'.mtvirus rck'iv..'r'' PoDairu3ca
numbcrof RNAvirus.'' hav. long filarnctrous vi.ioc. with hcli-
lig. 3. Phylo86y &d clsifiodon of Picn-liL vitEr d, Phylosdlic l@ of
i@n.lil. vi'lg dnM lon. cldric $.lrt of 100 .li8t d sitb ri& fom tlE mn
dsr.d Egid of tlE yiil rolt@ Gng P&OI?AIS: h.!dr kt{08 e mt &.s to
sla TVMV (r* Fis. r) TEv: robco adr F.wiu: C'MV (E E8. l): FMDV: f@!
rn-M6 di!.e icodvios EMCV: .'r..dJontddiri vio$ TllEv: Th.iLrr
mwir. ..eph.lomyEdilir viru* Pv3.Srb: poliovin. 3 S.!in rnini Pv2'Mrh: Polidi$3
2 M.h*y nBi.: HRVr4: hun6 rhinotiE! la: HAV: h.Daidr A viros, vitut tmily/
goup Mq s ihoq i. qTit lli rlud.d rcgios indiclrc divilio of pidruviNs i o
Eromhic B@p. b, Phln6b.r!." ,, cuEnt |domnic tstin$ of Pory-, coFc !n
pic.rEvilrg, H.t. A: hct{ili3 A vinr 6r&kie 6rEch. virus, td or tE gou3
grsoti.6, pdogaic ldi.rd mie
(b)
sd-Al,ir@.Ttatk iIrit w.t6tap vot.& Ap,it t99o IEJ
rh. picornrvi@ - ftus rhde ald
seleral
othcr
vit1lg mly conv.nin yt
lo@ly trcup.d in a picom.virulikc
luFrfrmily d rup6-sup.!9.oup.'! A
phyloso.ric tr@ caicuhcd f|m @rc
Ee, 4. SuFrfailjn'poly.
hd. ElaiffihiF bcrsa
viDs Phyl%di. E &rh
re. cLdiric adt.i. of
treEir *4u@ .Lb &rivcd
from Ef. 15; scqumt vG e
align.d srd all
phylogcnaiolt
uinromlivc cba.cd (ui-
quc
cn.d6. iddtic.l d@
cE)Frctd b.J@!drn3
usi.8 PROPARS, Nor.lh.in-
vdri6 of Pdy- .ld Cono.
viros Eldjvc ro
Fig, 3z; this ii
PFbrbly .hc !o
d'. s.ll d.L
d (rbour
l0 crEda F
|.rd). BMV =
brle odic
hotutiruq CMV -cuonbd
nosic oodovidr; AMv - .l-
falt! nosnc vinq TMV - lo-
b&@ ndic rob.mvidlr Sind
- sindbi! tinr nphlviru!
----L
subsequcnrly
cvolv. indcp.ndddy of onc
Polym..a phtlo8ed.s
k cqld b. pGtuhted
rh|r rh. rc?ticsc
flNtion ot all RNA viruscs
i! u ancimr
col@o! cvoludonlly fctnnc Prcd.rjnt
'casrl. rss.nbly, 6 n is rhc bais for
ub .risE. of ths vitlls, .!d prob.
.bly.volv.d only d@.' Onc my draw a
ncal phyloS.n.tic 'tcc on fic basis of
sinjluitics in polyM. lcquDc for
two suFfmilics of p6niv.-s@
SRNA viruscs
frco U. *qu6e cdpr,
.is d.t ot Domicr.r d.,'' th.t apF.B
to rener lhc
Fesumcd
liDq of decnt in
tetu of rwo oi rh. majd sup.rsDup-
iltj dcenb.d aborc
(s.. Fig.4). Ths, n
ln.y only bc resary o s.qucee shod
r.Ei6s ot vins gmm6 - .!d UEn
inf.r protcin
scqunces
from thqc * in
ddd ro bc lblc !o classily ncw virus.s
confidddy iolo dtablhlE l luFrldiliB,
rdilis rnd cvd sffi, or r.& h4rir o/
p
o
It
M6. 1
r.
p
I i c 6 e
8.
n.s
o
"lt.
Vlrus
Dhylog.ny
md cla$lncltlon
Thc nrin Fobld wirh rh. higrFr
clssitiqdd of viruss i! th dy simplc,
hic@hical phylotay-bas.d sysrn for
lhc simplcr viruscs
musr bsk down .t
ldt paniauy
sbove
r ccntin lcvel r/ d.
wlbt. g.^.n it co6id2t.tl: il tlE
rdplcs 8ircn abovc, clasifiqridr
.bov. trl prc*,t 'frnily lcv.l (o.
!uP.8rouP,
ror Plet viru$t beo|nca
v..y diflicuh as rehrionships cu rc
ldSq bG
tr.cld in .Dy hidehic.l odcr,
bcqe of tlc i mindint of ch.r&-
taisdcs dt|l lo dirdor colnbiFri6 of
ccn.in bsic modul.!. For i6r!lEc,
rhqld mc grcup u\c Come, Pory- .nd
picm.virus in orc slpcrf.mily, and the
-ctr'v
miro acid squlr@ sihilaritcs bcrvcc.t
dE presuscd Forss of Pory-, Cmo-
.nd pi@mrvirus is shoM in Fig. 3.
Trlis mtdy lhoei dE colllmn orisin (of
this
8d., .t l.ar) of rhc lhr.. soupr, y.r
ale dividca thch inlo rco8nislblc eir!
coBpording Lo
lhe t'oups d fdilics.
Whar
is m@. ir divid.s lhc pkod-
vilws into trcupings which .e@ r&r-
ly with lh6c propGed by AE Palrn6-
berS'' aflcr c@pdiens of rhe errkc
8.nom.s of U. viru&s. and which cur
.ighr .closs trldidd.l classificlrioN of
tlE vitu6 b.s.d on biolo8ical
sd pbysi-
c.l Fop.rfics, $ch d 'rcid srabiliry'
|.ld
tu'e or infe$od (*c Fi8.
3b). Tht i5 .
very g@d illushridr of the powd of
squdce .nalysis in lhc cldsificaion of
qsaims: a.lysis of orc p.rl of a @n-
sded tcrc yi.lds v6y simild Bulrs ro
aalyss on .ndrc tcnomic
scq@nc6,
od simulhcoalysivcs a more accunrc
pictu of rhe
pbylogeny
of rhe virusca
th.f, uy rmonr of mopholosical
dala
The l.s$n ro b. lc@cd liom Dc
exmplca
abovc is rhar rhq. is appqnrly
! kind of casue' d modulrr
dolu-
(ioraly mehdis oprating *ith th.
siftpler viruB - ad prob$ly wirh thc
legd as wU
- wih dircdr @r.
moduls bcing the bais for . nunbcr of
virus supcriamilis." Thc picona.r'Cohc'/
Po{y nodulc is the Mcm-Pro{-Pol casr-
rc, *hich .$ci.res itsclt wnh diffmt
Prot.i$ - oc $t ol ehich is .Nlh.r
modul, rhc 'rkecnomain isomtric
capsid prorcin
cssuc ol Picoma-
.nd
Comvires - in dilTcmr vi|llg.
Anolhd mrjot '$Frtdily - which
iftluda tlrc cnv.loFd, isofutric Alph!-
virus
snus
of thc dimslinfetins Totr-
virid!., thc rcdlik Tobmdirus, rhc
b.cillifm multipanir. dfrlf. mor.ic
virus trcup, !d th. iso|n tric mulrip.nn.
Bromo- md Cucumvnut s, sU of plers
- shde a polyln.rccrnrcl@ dbinding
protein corc nodul.." h hrs rllo reccluy
b.q prcp6.d th.t t ny nct.dv.-$N
SRNA viru$s m.y rlso sh@ snnil..
polynEru'3, .rd dFrc_foc c6rirur. ycr
rriothq '3updfmily'." Th. meh$ih
oi this
nodul.r .volurion
ir pobably
by
t.mmic l@mbindi@ (RNA-RNA rc.
Mbinatid in lh. ineacc' cncd),
which
dlows @r. tnodlld - *hich hav. pr.,
sumbly cvolvcd indepcndcrdy
- Io pick
up dircrcnt modules or irdividull
sencs.
ro r(h lcw disrirct virus that
will tlEn
Brcmo-, Cucuma, alfalfa m6aic, To-
b.m- and Alphavim!.s in eo{h.r?
Wr!! (h.n. of rh. siDildiry in cotr
Ptoteia b.tw@ Pory. .rd Tobaito-
vi'ws, Dd bcre-en r'y rcdlik d
tildentoB virior? WI.r of Lte
'c'sht
sroded eti.prallcl blta bwl' b8ic
rtrucmrl fc.rrc comon ro $. cqt PG
l.i6 of tl{ly .ll ismctric virid!,
rctddr6s ot shich virus
trcup tEy @mc
Phyloa.netlc
neteorkr
It should bc obvioa flom rlF t@toirt
(h.r uy 'wholc gemm. tr.. for rb.
vit@s will bede a nctvqk or clicu-
lated wcb ar or b.low thc sup.fMily
l.vel, s thc dir.Mr oridns of dilTercnl
pris of lh. t6oft h.rc !o bc 6@d .td
acknoel.dgcd. For .rmpl., Tob.rlo-
virus d Poryvirus
co.t prclcin scqucncca
nry convminrly
bc ued ro cl@'fy rhc
viru*s wiLhh rhe grdptlJr - yer rhdc
arc stong sirnilditiB in ltrucnr (if nol
in r.guft.) b.tv6 th. colt pro..irB of
vids of eval diffMr trouF ard
rupcrgrouF, rhar she no odlcr F5l simi-
tuidq! Shoutd onc pahlps uogni!.
oriy 'cor. ftodulc' similuiria ai bcirg
thc mosr phylog4ricdly irfl)lmriv!,
.rd g@p virus in hithcr trr| ..cordht
lo thir similarity in polyhq&s ard
N@iatcd rcpliclrior m.chinqf? I in-
clin. |osuds this vics. .s it is the corc
dbdul6 cGisrins of th. Epliqtid
lnlchiery .nd dj&dt tcEs th.t danu-
c.tc tlF dift@n snal.Si.s lv.ilrbl. to
viruss for h.ir .elic.tion. Evqydirt
cle in lhc tdde of r simplc viru is
.dc?..d fd $rvilal in diffc.! biolosicd
avi'1)l)llHB, .i in o.dc! to nU slishdy
dificmt nich6 ir th. wcld of lubclUulu
p.tDsd; ir
's
thc pollmrad dd a$o-
ci*ed machincry $at coatitut thc cs-
e@ of . Paniculd
gcDm. sEllc$r
tht
186 So4i^I,ica^lounatof5.brc. vot.E6 Ap,itl990
68. 5. PortibL 'mtwort' di.am3 b illusdc ridr El.!6$ipr. d, Ndwk di.etm
Cewins ov.dnd posibl. @d pldcin ad Flymce phylo8..i.r tor th. lsc virs s in
68. 4. Thji e! dEn for ill$dio q y, ed *s d th. sult ot ! tn/ogdic adltiti
GldimshiF e@ inlcrEd frcm.d. ad diagmr p'M!.d in Eft E !d ll. NoE rh{
vitE in G fdily (6 s@p) tre tlE s. baic @.r pFr.in dd polyll|rc modllB,
!fiil. ap.rlmili.l r.llid do d |rcsily. r. A nDdulc linLg. di.gm inusdi.g
hoe di,Id vitug e nE& ur of difi@r d3 of modlls. For c:upl.. Pdyvirug h:t.
. robmvifl yp. rud6t FDki., a pimvital pdyFc@ cotE, ed . rodlilc sd
pd.in .rd T iphid'ldmlnd h.lF pr@i4 piohrvirs h.rc . Piw Pol @
$d ! lhr-pren 'smdnc co! BMqruc hw. ! bDnoryt movmd Peir, e
.lpha pol @E and ! I .pDlli. iton&ic cd.
@mPN dd @E4r rhc PhyloScnicr ir .
simillrwly to U@ $ss.srcd h.rc.
Thir diclc rdd out a & d&s 10 rh.
Evobti@&y Dis$i6 Cop of th. Wcnm
C.F, I rh&l Tin Coe td hi. h.lp .nd
ciricih in itt pepadim,
L Cb*. T.M. (1933). Mok !r.. v.. ndplt lo.l/
i. to!.dii: r .o<n@st, TEd. X.
s e. s. r,|t.,...4 r't - )4 -
2,bn. S,rt.. Dr*ll ,E. B.J r* D. Dil
Csparu A. 0973)- C.s', Y'1!r'p, tr .dI,
3. Mwplry F.A- 6d rualbl'! D.w- (1990),
vito!
efty. h Y.iorop, 2.d .nn. .t4. a F. , -
!5. .!i. a.N. Fi.ldr ., cr Rrv6 Pr.!, Nr!
,1,
Md.e. R.EE (1934). Cl|t3ifidi6 sd
n6.ict.oc of vitu&3: Fo{rh Epd ol $.
Iddionrl c.nni@ oD rd66Y of
Videt. r,.4s,88.1.
t. stus E.C., SU|u J.ll. Dd L4iF AJ-
(t9ft). virut dolurid. tn vnolot ,2td.4t.,
.dn. B.N.licl&d,r RrEi Pr6.. N.r Ydt.
6, Cor N.J., BL.r Rf,l. Dd K6dd .P.
O9l9).
Pln*rt oa cv.rurid o( iinq.a A (lllNl)
vnusr n6 lt1 b 1936 3 ddmi..n by
oltoicho.jd. nr!?h! ud rru*irr odi.r
l. ta vnot 70,299-313.
7. Ri4Hsc R. (l9o)- M.lallr .voldtm Dd
di*ibdionoa dssE vird !rp. I !d rypc
Z
itr
^&c, vn ob A l7 t, 17
9
- 491.
3. Shutl. D.D, rd wid C.w,
(1939),SbcEEor
pdlairr dd Feis md i! rpplidior io rh.
eiomyof rhc F9vadrlFup. /r'. v,ts l.r.
9. Maar 4.F., tlmi& s.K. rd M.ro S,X,
(190?),
Plr! Yirus. rhi i*nbk ticm.'
rt!*!.li Ptc v th ltuaeL:o,.tco^3t.n 4
vi,otoot.t1tutu,^h*A
10. Cok6.cr &., EtF R., k xdnd
^.,
v6 P.
Dd w.[.ir r. (lerD_ Ercrurm or duesud
vtus. ti Pt& vutt tfuMtioratc^tt,4
rirotoo.En@a^..Aha!-.
ll. Coldb-r, R. (1937). G.,q. rimiltiri
bdre pld Dd Dim.l RNA vitort. &(ro'
12, ro Kema A, rd Eslq H.I.L.
(1914.
Tno
r?licrds or .ot".r sodc tiruL ,irE rrr, 5,
t3. Rdnor M.G.
ad R@kd R.R.
(193?).
whd
de. $. 6oldb. d.d o( vitus di u
rlo( vtn fbcnd.? lrd.,l.r 5.': ,ll,205 -
r.. Buj!.li ,J, .!d K'..b.'! P. (1916). C.cri
E6bi'db. Erlq &\A c6Fr.s oa r
n![iF,riErhlrvro/lr'ds.,12I,t2t-5]1.
15. Doia LL, Sh., i.O_ rd Rndd, R.A
0
$4.
Pdyvn.r F*ir! sh- sino aic 4q!.e
i@ololt rilh piin!, cdc, rd diica
r t d p1*i^. v
iato o r5t,fr - 71.
16. P.lda$6.
^.c.
(le8e). scqutr. ditMoB or
pam.rn.l clFa Fe6.. h Mok'b'
Atp.a 4 Pi@t6rtu It cn6 .rd D.Gti.^,
.!i, B.L s.dl.. ed E. Ehallt, ch+. 13.
Adsn!! Seic, fd MicFbiolol'.
17. Trdo N., PcI o', Emim /{,. K.nn o. xd
Ro3s F. (lrtr). cdplcad of t!. nbi.r
v-u ta6. ..q!.e d.ranhrlio: hjott
6R.a d6.jd mdr d. L lDdF4)
F*iIr ol uel'|nr.d ftraE-'hd RnA
vi@. Ytorr!,155.565 -576,
ll. Cibt A. (lgao). Hw ei.r e th. btrne
rrvr? I@not
',tr\
ro| - ld.
19. Milrd LH.
-d
AlEll RH. (t 9o)- Il.r.tin C
vnl'h'6ni.o-jdiqlcEt'li|rir,yi|h
Ftivi0s -d
nwjvhs a *ll a smbsr
oa
r*o plut vid. $p.4oup3. Pd. d.. l6d
S.t U s.,1. &7,2057- 2061.
helps to dcla. hithd 8rcupin$ oi viru$
* gowaer, tudically diftdenr app@ch'
B ro cosrucrid of rcladonship dmdc
gta6 d oth.r d+iclioB ol rcla'ionships
betw6 wholc virus tcDomcs could be
eful in depicrin8 'nctwdk phyloe@ia
otE f(m.! th.r @uld bc h?lpful is depicl
!d i! Fit. 5a: this corris6 of ovdlayins
ElatioBhip dddrctt!ru tor dilTo@r
t@s oi . D6bcr of virus groups or
fdili6i th. infoftnrtion cdld al$ be
dpicted in thrcc dimcnsiotr. Anothd
vry ol dcpictin8 reladonships berwem
whole gerctrs involvcs hodulc linkase
diagrams (*. Fit. 5r)i howcvcr. it could
bc@re nesay lo ue @rc thatr three
dimsbc in ods lo dcpict @dpler
ElttioBhiF !.tisf.cldily. Ir is wGO
mtinS lh 0t. vcry Eorly *quoccd
homa! hc?.tiis C vin!3 .ppcG lo sh@
farEs of bolh picdnavirus'lik and
.lpi.virulik sup.rf.FtilieJ': ilt poty-
tlEre is rldcd |o rhosc of rhe alPhaviru
suprfdily, qhilc oLhq prctciB rc-
smble tt6sc of the pionavitulike
superfnily, ehich m.kc it an er@llent
caDdidaE for . nerwork phylo8dcric
h appca obvioa th.t ey futute ap
F@h rc lh. clainc.ti@ oJ vilws -
ard oe hop6 ir will bc ! unihcd ap-
po&h. a 3imitanti6 bcrr6 vioes
appcf sfonS.r rhln bcrw4n rhe diffcMr
Iroups of p@plc who study ftcm - will
sins or lalq h.vc lo r*c inro lccount
lhrt cl$sic.l rpprcrchcs
ro cl4sification
ar! not ruitlble fd viruses, d .itid
hic.a.chics
camot b. imposd on ort.-
dsm rhar app.d
- evolution{ilys?.rk-
irt - ro h.vc bc.D rlthd pl1mi$uols in
shdinS thcn chadlgisrics doltd.
R.rh6, vi.olotic.l systmadsB (a ne*
sd r.r! brc.d) should adopr a flexiblc
wait-.n.t-s4 .pproach, ed eet hiqd-
chi6 or y *hc the d Mmbituoudy
obvious: Lhie
rcd waiting
for $qu.m.
irfomado otr a l.rge number
of viruses
of humiB, pl&l5, lnilruh, rbgi dd b&-
rqi.. ed pdlorming dctailed
amlyss of
similande at borb the nucleic acid and
protcin s.qucrc. ldcl, b.l6e cven ar-
Gmptint to cl*sity .Dywh* above th.
sroup
d subjahily lcvcl. viro s'sEma-
tisrs should abo pcrhapi
b n@ ncrible
than thck ccllul.! co{lterpdts. ard tor bc
fri8hrcncd
or by hkjnt phylossrtic nct-
*dks a wcll as simplc '16 inb @n-
siderarimfo! chrsilicarioB.
Thc tinal lso is thlt virur s]stema-
rics
(sd systcmatists) should
rcned (dd
rcflecr 6) rhc erFcmc divdny ot virus
tenome3.
.nd thcir obvioB and prcbablc
iDt.rcl|tioruhip!, in clasilicati@
shmc! th.t arc auitd
to th organism
bcils clBificd. rt'd nor dcrivtd sttdghr
f'm $c wodd ot ceuuld organism!.
Classifid of ccUulu orseiss *ho
bcSin to u$ $qum@ d.u Fi8ht al$ t|rc
tutc ol $c po{cntial f6 muldplc
tid6 of
dcsnt ol difIeMr elluld Ggdcllcs.
spc.irlly of pl ts. Wilh $@ Fnomcs
lo play
with
(nuclq!.
lnitehddrial tDd
chldoplaD. ir Fly be itrqsting lo
zP. -,sc Cr l:::nrj aF)
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... But the boundary between these two categories seems to be blurred by the discovery of virus. The viruses are considered to be 'at the edge of life' (Rybicki, 1990). Recently, the discovery of virophages (Pearson, 2008), the fact that a specific kind of smaller virus infects and parasitises bigger viruses, suggest that viruses are a kind of life form. ...
Thesis
Chinese languages have a set of segments known as ‘apical vowels’ (舌尖元音 in Chinese). Their exact nature is still the source of an ongoing debate: Are they consonants or vowels? ‘Apical vowels’ have been analysed in previous studies as genuine vowels, fricative vowels, syllabic fricatives, or syllabic approximants. This dissertation is concerned with the apical vowel attested in Jixi-Hui Chinese. I examine this segment from phonetic and phonological perspectives and show that it is best defined as a voiced fricative consonant (transcribed /z̩/).Phonologically, this segment is a distinct phoneme from /i/. It is exclusively attested in syllable nucleus position where it constitutes a tone-bearing unit. It can appear not only after coronal sibilants /s ts tsh/, but also bilabials /p ph/ and nasals /m n/. Phonetically, the acoustic and articulatory characteristics of this segment are examined. The results show that /z̩/ contains in the majority of cases frication noise in its initial phase superposed on voicing, and a clearer formant structure appears towards its end. The harmonic-to-noise ratio and zero-crossing rate analyses confirm this significant presence of noise, clearly distinguishing this segment from vowels. The smoothing-spline ANOVA analyses of ultrasound data show that /z̩/ has a near-identical tongue shape to /s/ on both mid-sagittal and coronal planes despite some speaker-specific differences. This /s/-like tongue shape is constant in bilabial and alveolar consonantal contexts.The variability in the way /z̩/ is phonetically implemented is argued to be a consequence of two interacting constraints: a structural one related to the distinctive status of /z̩/ and the role it plays within syllable structure, and a physical one related to the incompatibility of voicing and frication. The study further argues for the necessity of recognizing syllabic fricatives in Jixi-Hui Chinese and probably also in other Chinese languages.
... Advances in biological understanding since the time of the so-called 'modern evolutionary synthesis' or 'neo-darwinism' of the 20 th Century are an additional consideration for the practical application of evolutionary biology. For example, the actuality of prions as evolvable proteins (Lindquist, 1997;Wickner, 1997) and the character of viruses 6 as non-organisms and "entities at the edge of life" (Rybicki, 1990;Murphy et al., 1999) came onto the scene only in the 1990s. Viroids, subviral pathogens of plants (Diener, 2003;Ding, 2009), are a further concern. ...
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This pre-print relates to a concern that a common understanding of the theory of evolution by natural selection may be impeded by English (or any other language, for that matter) as the current vehicular language of science. The concern is heightened because much discussion in evolutionary biology is characterised by figurative rather than literal language. Natural selection theory is valuable in understanding the dynamics of infectious disease and linguistic issue may impair the interoperability of the world's veterinary services. These services are have heightened value given devastating zoonotic pandemics like COVID-19. The target audience is FAO and OIE. Early action is needed and this incomplete draft may excite interest.
... Whether they should be defined as beings in their own right is a matter of continuous debate among microbiologists (see for instance Rybicki 1990;Xue et al. 2010;Casiraghi et al. 2016). ...
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In the course of 2020, two viruses, COVID-19 and African swine fever, set in motion powerful border (de)stabilizations. This chapter makes the case for an understanding of borders which integrates the complex interactions between humans, viruses, animals, objects and technologies. It develops an approach to bordertextures that regards them as more-than-human compositions, spanning a multitude of both human and nonhuman actors. These actors are bound up in relations of power; relations that subsequently materialize in border (de)stabilizations. The chapter places a special focus on two groups of living nonhumans that have yet to receive the attention they deserve from border researchers: viruses and animals. How do they shape, respond to and operate independently from border control?
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Since the emergence of yellow fever in the Americas and the devastating 1918 influenza pandemic, biologists and clinicians have been drawn to human infecting viruses to understand their mechanisms of infection better and develop effective therapeutics against them. However, the complex molecular and cellular processes that these viruses use to infect and multiply in human cells have been a source of great concern for the scientific community since the discovery of the first human infecting virus. Viral disease outbreaks, such as the recent COVID-19 pandemic caused by a novel coronavirus, have claimed millions of lives and caused significant economic damage worldwide. In this study, we investigated the mechanisms of host-virus interaction and the molecular machinery involved in the pathogenesis of some common human viruses. We also performed a phylogenetic analysis of viral proteins involved in host-virus interaction to understand the changes in the sequence organization of these proteins during evolution for various strains of viruses to gain insights into the viral origin’s evolutionary perspectives.
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Political decisions, constellations, and behaviors exert a large influence of the dynamics of the severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2) pandemic. Politics influences the choice of containment policies and the compliance with these policies—and therefore ultimately the epidemiological situation in each country, state, district, or even neighborhood. This introduction puts the articles collected in this special issue into the broader perspective of the social science literature on Covid-19.
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