bigram

This is a table of type bigram and their frequencies. Use it to search & browse the list to learn more about your study carrel.

bigram	frequency
codon usage	238
infectious bronchitis	191
amino acid	181
ck ch	145
bronchitis virus	145
respiratory syndrome	119
acute respiratory	110
phylogenetic analysis	108
severe acute	87
genetic diversity	85
phylogenetic tree	77
cell epitopes	73
ibv strains	69
closely related	69
syndrome coronavirus	65
spike protein	63
usage bias	62
amino acids	61
novel coronavirus	55
synonymous codon	51
complete genome	50
avian infectious	49
genet evol	48
doc id	48
evol doi	48
rna viruses	48
infect genet	48
cord uid	48
sars coronavirus	46
respiratory syncytial	44
maximum likelihood	44
genome sequences	43
vp gene	43
nsp proteins	42
sequence alignment	41
ns protein	40
syncytial virus	39
accession numbers	39
ch lhlj	38
usage pattern	38
middle east	37
open reading	37
molecular characterization	36
natural selection	36
japanese encephalitis	36
sequence analysis	35
peptide vaccine	34
stranded rna	34
positive samples	34
population size	33
present study	33
public health	32
coding region	32
nucleotide sequences	32
recombination events	32
south korea	31
fecal samples	30
genome sequence	30
east respiratory	30
molecular epidemiology	30
chagas disease	29
viral rna	29
infectious diseases	29
pcr products	29
respiratory disease	28
vaccine strains	28
borrelia spp	27
reading frame	27
immune response	27
host cell	27
performed using	27
gene sequences	27
influenza virus	27
rna polymerase	26
reemerging korean	26
supplementary data	26
phylogenetic trees	26
structural proteins	26
fekov strains	26
leptospira spp	25
spike glycoprotein	25
lhlj vii	25
genbank accession	25
previously described	24
binding domain	24
human respiratory	24
sequence data	24
strain ck	23
coding sequence	23
human coronavirus	23
cell epitope	23
group i	22
reference strains	22
wild birds	22
journal pre	22
sudan ar	22
dengue virus	22
viral replication	22
virus type	22
bat sarsr	21
field strains	21
rna virus	21
mutation pressure	21
orf ab	21
immunodeficiency virus	21
genetic variation	21
receptor binding	21
supplementary table	21
hexon variants	21
korean pedv	21
host cells	20
coding sequences	20
di martino	20
multiple sequence	20
reverse transcriptase	20
structural protein	20
ck sudan	20
host species	19
avian influenza	19
strains isolated	19
vaccine development	19
nov strains	19
avian coronavirus	19
nucleotide sequence	19
polish ibv	19
nucleotide identity	19
species transmission	19
genomic sequences	19
viral proteins	19
world health	19
whole genome	19
type strains	18
recent years	18
immune system	18
south america	18
disease virus	18
accession number	18
found online	18
evolutionary genetics	18
nucleic acid	18
analysis showed	18
pedv strains	18
southwestern china	18
reading frames	18
large number	17
synonymous codons	17
highly pathogenic	17
aliphatic amino	17
fruit bats	17
vaccine strain	17
different genotypes	17
analysis based	17
human sars	17
type i	17
infected cells	17
acid sequences	17
bootstrap values	17
cov nsp	17
vp protein	17
comparative analysis	17
nipah virus	17
sequence identity	17
respiratory tract	17
secondary structure	17
respiratory coronavirus	16
rp patients	16
innate immune	16
human immunodeficiency	16
frame shift	16
coronavirus disease	16
health organization	16
previous study	16
also found	16
protein synthesis	16
pcr amplification	16
mutation rate	16
usage patterns	16
coronavirus nsp	16
capsid protein	16
reference sequence	16
gene expression	16
ch scyb	16
phylogenetic analyses	16
accessory proteins	16
molecular evolutionary	16
population dynamics	16
enc values	16
viral infections	15
authors declare	15
constructed using	15
molecular evolution	15
encephalitis virus	15
previous reports	15
protein sequences	15
southern china	15
innate immunity	15
mouth disease	15
orf gene	15
dependent rna	15
previously reported	15
immunogenicity score	15
genome segments	15
nested pcr	15
like viruses	15
lyme disease	15
bat species	15
strains ck	15
complete vp	14
lao pdr	14
pcr product	14
rotavirus strain	14
korean strains	14
infectious disease	14
clinical samples	14
like coronavirus	14
viruses isolated	14
canine respiratory	14
ebola virus	14
interspecies transmission	14
important role	14
rva strains	14
united states	14
porcine epidemic	14
bronchitis coronavirus	14
rotavirus strains	14
protein gene	14
nucleotide substitutions	14
genbank database	14
cruzi infection	14
like virus	13
nucleotide polymorphism	13
acid identities	13
polyprotein gene	13
genomic rna	13
single nucleotide	13
previous studies	13
newcastle disease	13
pathogenic leptospira	13
analysis revealed	13
point mutations	13
vaccine design	13
virus infection	13
protein structure	13
using mega	13
viral genome	13
human influenza	13
fd ita	13
virus strain	13
trna pools	13
bronchitis viruses	13
significant difference	13
genetic variability	13
genomic analysis	13
highly conserved	13
skyline plot	13
horseshoe bats	13
nonstructural proteins	13
ch lnm	13
guangdong province	13
host innate	13
vp sequences	13
hong kong	13
genetic characterization	13
genetics analysis	13
samples collected	13
cai values	12
aligned using	12
ecological processes	12
sanger sequencing	12
prm protein	12
acid changes	12
grant number	12
acid sequence	12
early epidemic	12
northeast china	12
bat coronaviruses	12
two strains	12
conserved regions	12
aa identity	12
joining method	12
nt identity	12
ch ldl	12
civet scovs	12
genetic characteristics	12
field isolates	12
chz china	12
virus genome	12
transfection assays	12
new coronavirus	12
canine nov	12
pcr assay	12
coding regions	12
thermo fisher	12
emerging viruses	12
coronavirus spike	12
i coronavirus	12
population structure	12
core protein	12
like strains	12
avian coronaviruses	12
optimal codons	12
acid composition	11
functional sirnas	11
fisher scientific	11
strains identified	11
ibv isolates	11
divergence times	11
host immune	11
synonymous mutations	11
borrelia species	11
gene sequence	11
common ancestor	11
human populations	11
canine parvovirus	11
nucleotide composition	11
converting enzyme	11
nsp genes	11
complete polyprotein	11
genetic analysis	11
fruit bat	11
recombination event	11
immune responses	11
nonsynonymous variants	11
novel human	11
diarrhea virus	11
phylogenetic inference	11
evolutionary history	11
infected individuals	11
global spread	11
tioman virus	11
first report	11
epidemic diarrhea	11
genomic sequence	11
calculated using	11
rna recombination	11
bootstrap replicates	11
final extension	11
borrelia burgdorferi	11
generated using	11
first identified	11
antigenic relatedness	11
ibv strain	11
positive selection	11
human scovs	11
commonly used	11
ev strains	11
tree based	11
virus replication	11
substitution models	11
indian sars	11
codon adaptation	11
time scale	11
purified using	11
among different	11
analysis using	11
substitution model	11
overall codon	11
virus transmission	11
rrna gene	11
early polish	11
net charge	11
ibv lineages	11
ch scdy	10
positively selected	10
molecular characteristics	10
coronavirus infectious	10
complete genomes	10
cell entry	10
bat sars	10
bovine coronavirus	10
trypanosoma cruzi	10
influenza viruses	10
respiratory distress	10
late epidemic	10
bayesian phylogenetic	10
host range	10
subunit gene	10
cell culture	10
kidney samples	10
recombination analysis	10
nov strain	10
sample size	10
connectivity index	10
polymerase chain	10
vaccine formulation	10
molecular clock	10
chicken eggs	10
first time	10
chinese fekov	10
genomic characterization	10
nucleocapsid protein	10
also observed	10
respiratory infections	10
highly divergent	10
sequences obtained	10
likelihood phylogenetic	10
orf encodes	10
blood samples	10
stool samples	10
new zealand	10
whole coding	10
specific primers	10
cdna clone	10
genetic drift	10
virus strains	10
may play	10
boman index	10
also identified	10
chain reaction	10
viral entry	10
epitope prediction	10
results showed	10
bat origin	10
rapidly evolving	10
chicken flocks	10
vp genes	10
three different	10
genome analysis	10
likelihood method	10
better understand	10
gene source	10
mutation points	10
norwalk virus	10
high mutation	10
national veterinary	10
social factors	10
bayesian skyline	9
genomic diversity	9
life technologies	9
international committee	9
virus isolates	9
type strain	9
cleavage site	9
supplementary material	9
hypervariable regions	9
rna replication	9
porcine kobuvirus	9
ch cqkx	9
human strain	9
bactrian camels	9
vero ccl	9
binding affinity	9
electron microscopy	9
human enterovirus	9
bayesian inference	9
genome sequencing	9
consensus sequence	9
selection pressure	9
genetic recombination	9
polish strains	9
results suggest	9
major hexon	9
urban genotypes	9
canine norovirus	9
human novs	9
us strains	9
canine infectious	9
fekov strain	9
length genomic	9
fekov reference	9
ibv genome	9
ace receptor	9
feline calicivirus	9
different countries	9
assembled using	9
hypervariable region	9
primers used	9
acid identity	9
applied biosystems	9
different ibv	9
relaxed clock	9
cropland cover	9
ace expression	9
primer pair	9
bovine kobuvirus	9
full genome	9
enc value	9
bkov vp	9
nt aa	9
better understanding	9
reverse vaccinology	9
southeast asia	9
maximum parsimony	9
escherichia coli	9
feline nov	9
population history	9
analyzed using	9
hiv infection	9
rna genome	9
anhui province	9
acid residues	9
membrane protein	9
dna sequences	9
urban ducks	9
nucleotide substitution	9
spike gene	9
selected sites	9
cdna synthesis	9
polish gi	9
recent studies	9
nt duplication	9
close relationship	9
complete genomic	9
sequences using	9
clustered together	9
bayesian coalescent	9
like ibv	8
aichi virus	8
clock model	8
canine coronavirus	8
positive rate	8
infected patients	8
feline strain	8
nucleotide contents	8
two different	8
genetic heterogeneity	8
host protein	8
hydrophobic residues	8
epidemic scovs	8
genogroup gvi	8
ba genotype	8
veterinary institute	8
rva strain	8
type ibv	8
clinical signs	8
replication fidelity	8
national center	8
bactrian camel	8
canine feline	8
sequence variation	8
vp region	8
recurrent mutations	8
diarrhoeic cats	8
fcv orf	8
extracted using	8
emerging infectious	8
human ace	8
healthy dogs	8
canine strain	8
rva rabbit	8
bari ita	8
simple method	8
nl nsp	8
parainfluenza virus	8
different strains	8
south american	8
step rt	8
viral diseases	8
rna synthesis	8
human transmission	8
ns proteins	8
acid substitutions	8
human norovirus	8
entire genome	8
like strain	8
mutation rates	8
selective pressure	8
extraction kit	8
new genotype	8
domestic cats	8
agarose gel	8
bat coronavirus	8
recent common	8
four ibv	8
evolutionary rates	8
family coronaviridae	8
recombination detection	8
nucleotide identities	8
total rna	8
epidemiological models	8
publicly available	8
cell lines	8
highest nucleotide	8
immune sera	8
nt deletion	8
flab fragments	8
murine coronavirus	8
north america	8
sir model	8
indian patients	8
protein vp	8
strain te	8
takara bio	8
wild animals	8
host population	8
zoonotic viruses	8
patients infected	8
feline kobuvirus	8
mouse hepatitis	8
human host	8
five proteins	8
sequence identities	8
infectious respiratory	8
allantoic fluid	8
illumina miseq	8
time rt	8
norovirus infection	8
ch scms	8
illumina sequencing	8
major role	8
class i	8
epidemiological studies	7
adaptive evolution	7
respiratory diseases	7
binding site	7
strand cdna	7
missense mutations	7
membrane fusion	7
viral strains	7
peptide vaccines	7
flab gene	7
potential epitopes	7
pcr kit	7
tested positive	7
east asia	7
highly variable	7
like coronaviruses	7
virus infectious	7
reference sequences	7
full genomic	7
clinical characteristics	7
may represent	7
hepatitis virus	7
one synonymous	7
lower respiratory	7
cek cells	7
dna polymerase	7
respiratory infection	7
nt sequence	7
agilent technologies	7
differential equations	7
bio inc	7
neutralizing antibodies	7
pp ab	7
chn sccd	7
strains detected	7
statistically significant	7
codon bias	7
aa sequence	7
chinese horseshoe	7
strain isolated	7
genetic susceptibility	7
two distinct	7
across populations	7
virus population	7
may provide	7
amoy gardens	7
infect humans	7
software package	7
pca analysis	7
low frequencies	7
forest cover	7
significantly different	7
tissue tropism	7
antiviral therapeutic	7
virus rna	7
demographic history	7
purifying selection	7
model parameters	7
younger brother	7
rva dog	7
human population	7
per site	7
distantly related	7
settlement cover	7
genome organization	7
software version	7
reverse transcription	7
wetland cover	7
significant differences	7
natural reservoirs	7
likelihood phylogenies	7
mutated reads	7
may also	7
respiratory illness	7
cell line	7
different host	7
rabies virus	7
diagnostic tests	7
basic reproduction	7
corresponding amino	7
burgdorferi sensu	7
nsp protein	7
cov infection	7
shannon index	7
epithelial cells	7
length genome	7
south africa	7
biotechnology information	7
study reported	7
lpv rtv	7
stool sample	7
land cover	7
east asian	7
antigenic epitopes	7
evolutionary relationships	7
san diego	7
markov chain	7
fragmentation index	7
results indicate	7
tc chn	7
important reservoir	7
animal species	7
infectious cdna	7
generation sequencing	7
study showed	7
deep sequencing	7
east region	7
transmissible gastroenteritis	7
multiple alignment	7
therapeutic drugs	7
substitution rate	7
molecular evidence	7
purified core	7
kcal mol	7
breakpoint site	7
virus isolated	6
previous report	6
clock models	6
genetically related	6
zoonotic transmission	6
buffered saline	6
genomic dna	6
sequences generated	6
urban cycle	6
zika virus	6
principal component	6
receptor recognition	6
colombian population	6
like human	6
viseu prt	6
monte carlo	6
predicted using	6
vaccinology approach	6
viral titers	6
gene analysis	6
population genetics	6
human aivs	6
genetic code	6
hydrophilicity value	6
crcov isolates	6
hek cells	6
sequences showed	6
endoplasmic reticulum	6
genomic location	6
region sequences	6
new variants	6
reproduction ratio	6
reassortment events	6
different serotypes	6
edited using	6
therapeutic drug	6
negative selection	6
three strains	6
swedish dogs	6
diagnostic purposes	6
acute gastroenteritis	6
ifng gene	6
coronavirus associated	6
substitutions per	6
virus evolution	6
phylogenetic relationships	6
american asian	6
human coronaviruses	6
united kingdom	6
unique aa	6
capsid gene	6
conservancy analysis	6
i coronaviruses	6
rscu value	6
sequence similarity	6
related coronavirus	6
transmission routes	6
national institute	6
nov genotypes	6
lapine strain	6
potential lineage	6
spike proteins	6
recent study	6
vaccine candidates	6
sars coronaviruses	6
highly contagious	6
systematic review	6
gene revealed	6
remains unclear	6
mammalian orthoreovirus	6
forest fragmentation	6
similar viruses	6
human cells	6
one strain	6
higher elevation	6
first two	6
gel electrophoresis	6
four genera	6
conducted using	6
serological evidence	6
ch scls	6
chain monte	6
human adenovirus	6
broadly reactive	6
darwinian selection	6
strains belonging	6
based peptide	6
reagent kit	6
asymptomatic patients	6
clinical features	6
european countries	6
camelus bactrianus	6
ncov proteins	6
screened using	6
virus nucleic	6
viral pathogens	6
virus using	6
homoplasic sites	6
conserved among	6
close proximity	6
ribosomal frame	6
structural genes	6
spontaneous mutations	6
strains showed	6
clinical manifestations	6
western blot	6
monoclonal antibodies	6
genogroup iv	6
new species	6
wild bird	6
qx strains	6
vaccinia virus	6
nsp gene	6
ibv ck	6
viral pathogenesis	6
vp sequence	6
porcine rotavirus	6
pistoia ita	6
evolutionary dynamics	6
rna extraction	6
bats covs	6
silico approach	6
separate branch	6
molecular biology	6
using trizol	6
interfering rna	6
length genomes	6
sampling dates	6
outbreak associated	6
analysis version	6
novel mammalian	6
parvovirus type	6
significantly higher	6
virus genomes	6
wild ducks	6
genetic variants	6
analysis reveals	6
mutated sequences	6
play roles	6
described previously	6
gel extraction	6
identified epitopes	6
mafft multiple	6
bat strain	6
bat viruses	6
default parameters	6
zoonotic origin	6
population genetic	6
serological tests	6
function variants	6
nucleotide similarity	6
ch scmy	6
allantoic fluids	6
borrelia spirochetes	6
lapine rotavirus	6
active sites	6
human infection	6
norovirus genogroup	6
first isolation	6
mutational pressure	6
molecular detection	6
healthy controls	6
relapsing fever	6
tc ita	6
identified using	6
used vaccine	6
wide range	6
mhc class	6
novel vp	6
lineage iii	6
borne viruses	6
sylvatic genotype	6
monophyletic clade	6
reservoir hosts	6
related coronaviruses	6
strand rna	6
suppresses host	6
canine novs	6
four major	6
natural recombination	6
epitopes namely	6
infection rate	6
batcov ratg	6
virus prevalence	6
dendritic cells	5
different areas	5
transmission events	5
primer sequences	5
virus genotypes	5
inferred using	5
amplified using	5
findings suggest	5
natural history	5
western africa	5
detection program	5
samples obtained	5
eidolon helvum	5
genotype strains	5
selected peptides	5
geographical regions	5
rate variation	5
strains collected	5
simplex virus	5
reference strain	5
major structural	5
sense rna	5
virus codon	5
risk factors	5
data suggest	5
information criterion	5
virus ns	5
ch lsc	5
urban population	5
water areas	5
adenosine deaminases	5
high genetic	5
gastroenteritis virus	5
two sequences	5
expressing plasmids	5
diarrheic samples	5
similarity degree	5
estimated using	5
urban environments	5
acid position	5
dogs may	5
close genetic	5
virus detection	5
deduced amino	5
percentage identity	5
pcr conditions	5
generalized skyline	5
turkey coronavirus	5
complete sars	5
china date	5
variants including	5
among children	5
genomic characteristics	5
pairwise aa	5
vn epitopes	5
evolutionary relationship	5
like particles	5
signaling pathway	5
two large	5
correlation analysis	5
uniprot protein	5
four structural	5
another study	5
strain cat	5
located within	5
like receptor	5
synthesis kit	5
attachment protein	5
migration rates	5
total number	5
purification kit	5
size history	5
study group	5
nucleocapsid gene	5
base substitutions	5
mini kit	5
genome alignment	5
recovered patients	5
cov spike	5
also detected	5
food production	5
deltacoronavirus supports	5
antiviral drugs	5
murine kobuvirus	5
coronavirus genome	5
autumn migration	5
nervous system	5
atlantic forest	5
two civet	5
rrna sequences	5
binding epitopes	5
viral diarrhea	5
human noroviruses	5
online tool	5
hydrophilicity scores	5
genetic relationship	5
herpes simplex	5
red list	5
hydrophilicity score	5
broiler chickens	5
genetic distance	5
polymerase gene	5
pcr using	5
pathogenic mass	5
transmission history	5
unique early	5
comparative genome	5
giv novs	5
antigenic characteristics	5
bar indicates	5
reference genome	5
us strain	5
significant role	5
veterinary research	5
sample sizes	5
detected across	5
viral infection	5
novel feline	5
anthropogenic environments	5
genus deltacoronavirus	5
peptide epitopes	5
cluster analysis	5
urban areas	5
analysis program	5
generation time	5
multiple reassortment	5
chemokine receptor	5
acid deletion	5
england biolabs	5
nosed fruit	5
protease inhibitor	5
mean age	5
rna binding	5
sequences available	5
fever virus	5
peruvian alpaca	5
across years	5
may affect	5
successfully obtained	5
study aimed	5
poultry flocks	5
feline coronavirus	5
seven novel	5
retrospective study	5
six months	5
loaded peptide	5
direct sequencing	5
also analyzed	5
high antigenicity	5
synthesized using	5
md values	5
protein information	5
viral spike	5
respiratory viruses	5
posterior probability	5
virus classification	5
spontaneous mutation	5
genetic changes	5
different parts	5
determine whether	5
signal transduction	5
related viruses	5
expression levels	5
high frequency	5
sequencing data	5
specific primer	5
negative side	5
epidemic strain	5
acute diarrhea	5
homolog proteins	5
untranslated region	5
overall prevalence	5
molecular analysis	5
net charges	5
genomic data	5
also predicted	5
geographical distribution	5
accessory protein	5
coronavirus infection	5
index case	5
gamma gene	5
coronaviridae family	5
pneumonia outbreak	5
west africa	5
adenovirus type	5
genetically diverse	5
human beings	5
domestic animals	5
using maximum	5
missing data	5
hvr encoding	5
usage variation	5
like infectious	5
viral cross	5
vp capsid	5
immunodeficiency viruses	5
using reverse	5
simian immunodeficiency	5
almost identical	5
research institute	5
throughput sequencing	5
respiratory signs	5
specific pathogen	5
poorly understood	5
population sizes	5
duplicated region	5
pathogenic viruses	5
three distinct	5
normal tissues	5
land use	5
transmission dynamics	5
genome backbone	5
protein kinase	5
genetic models	5
small number	5
determined using	5
avian paramyxovirus	5
rna editing	5
canine noroviruses	5
supports bat	5
final concentration	5
pcr results	5
egg production	5
water cover	5
epitopes using	5
novel respiratory	5
evolutionary rate	5
current situation	5
civet scov	5
feline novs	5
viral genomic	5
coronavirus avian	5
canine kobuvirus	5
phylogenetic reconstruction	5
qx ibv	5
strains circulating	5
previously published	5
severe respiratory	5
blood group	5
variation across	5
palm civets	5
natural host	5
sylvatic genotypes	5
bootstrap support	5
superscript iii	5
different epidemic	5
large fraction	5
acid level	5
allele frequencies	5
virus infections	5
coronavirus oc	5
possess high	5
effective population	5
evolutionary analysis	5
prevalence rate	5
mortality rate	5
mrv strains	5
new england	5
upper respiratory	5
total net	5
old female	5
using bioedit	5
highest immunogenicity	5
time evolution	5
pteropus bats	5
positive sera	5
potential recombination	5
independent branch	5
also tested	5
antigenic sites	5
wild migratory	5
confirmed using	5
site year	5
novel virus	5
two epitopes	5
protein genes	5
epidemic models	5
order nidovirales	5
using seqman	5
west nile	5
new model	5
done using	5
viral evolution	5
gene recombination	5
taken together	5
coronavirus ibv	5
natural habitats	5
hexon gene	5
pairwise comparison	5
global health	5
helvum bats	5
cell receptor	5
first molecular	5
gb strain	5
antibody responses	5
sequencing libraries	5
envelope protein	5
syncytial viruses	5
rab clustered	5
also performed	5
rva alpaca	5
antagonize host	5
structured coalescent	5
recombination within	5
nucleotide duplication	5
single open	5
viral spread	5
partial rdrp	5
fasta format	5
biological sequence	4
genetic predisposition	4
aksu city	4
option complete	4
i binding	4
seven hvrs	4
bigdye terminator	4
endemic korean	4
similar results	4
virus attachment	4
glycoprotein sequences	4
first strand	4
coronavirus strain	4
financial interests	4
bold triangles	4
remains unknown	4
commercial broiler	4
bkov genome	4
rna adenosine	4
epidemiological data	4
xinjiang province	4
sampling interval	4
serine protease	4
genome assemblies	4
hubei province	4
dnastar inc	4
least three	4
likelihood phylogeny	4
using anti	4
seven different	4
brazilian bats	4
highly immunogenic	4
virus disease	4
global diversity	4
paramyxoviridae family	4
first detected	4
feline norovirus	4
viral dna	4
two clades	4
broiler chicken	4
several genes	4
viral capsid	4
assessed using	4
fc cluster	4
necrosis factor	4
viral protein	4
acid differences	4
gene segment	4
menangle virus	4
borne viral	4
i interferon	4
hierarchical analysis	4
algorithms implemented	4
newly emerged	4
young dogs	4
orf junction	4
viral loads	4
mammalian species	4
influencing factors	4
strains available	4
probability distribution	4
codon position	4
phosphoprotein gene	4
anas platyrhynchos	4
studies showed	4
sars epidemic	4
novel bat	4
nt duplicated	4
binding affinities	4
identical amino	4
virus will	4
third site	4
using clustal	4
remaining non	4
online version	4
identified within	4
ibv isolate	4
takes place	4
positive side	4
trees constructed	4
strain detected	4
i ifn	4
viral genomes	4
accession nc	4
confirmed cases	4
showed high	4
cross species	4
jev proteins	4
statistical computing	4
young children	4
length human	4
default settings	4
limited understanding	4
novel group	4
divergence time	4
library preparation	4
cycle sequencing	4
ifn response	4
end reads	4
strain ita	4
fragments belonging	4
solid tumor	4
high similarity	4
species obtained	4
sudanese isolate	4
chicken embryos	4
phylogenetic methods	4
laboratory animal	4
spectrum antiviral	4
feline kobuviruses	4
novel genotype	4
bat populations	4
natural course	4
ten ibvs	4
strain ecu	4
dimensional structure	4
susceptible individuals	4
vp amino	4
respiratory failure	4
feline bocavirus	4
host shift	4
broad spectrum	4
canine bufavirus	4
immunocompromised patients	4
fecal specimens	4
model averaging	4
strains shared	4
antigenic determinants	4
hrsv infection	4
length vp	4
fusion peptide	4
acid substitution	4
gene coding	4
codon deoptimization	4
one serotype	4
substitutions site	4
akaike information	4
broiler flocks	4
key determinant	4
field ibv	4
epi isl	4
virus isolation	4
ca repeat	4
alignment search	4
confidence interval	4
leptospira sp	4
study revealed	4
antibodies specific	4
ibv variants	4
using bayesian	4
usage biases	4
viral transmission	4
southern sweden	4
ck za	4
gov blast	4
tissue culture	4
virus taxonomy	4
migration process	4
bstvs vs	4
aa mutations	4
phylogenetic profiling	4
control study	4
accession jx	4
aku aku	4
high risk	4
clc genomics	4
wide analysis	4
variation among	4
sylvatic dengue	4
effective number	4
intermediate hosts	4
base transitions	4
least one	4
strains previously	4
qiaquick gel	4
genetic relationships	4
severe diarrhea	4
evolutionary biology	4
uncultured leptospira	4
rapid replacement	4
cc shared	4
viruses belonging	4
multiple alignments	4
allowed us	4
dnase i	4
time pcr	4
high hydrophilicity	4
tissue samples	4
lower prevalence	4
genetic data	4
solid tumors	4
large numbers	4
four mass	4
immunogenic vaccine	4
drug resistance	4
pet dogs	4
human nov	4
iucn red	4
tract infections	4
blast search	4
bat covs	4
rna secondary	4
also known	4
following accession	4
human rva	4
samples across	4
studies suggest	4
demographic stochasticity	4
health concern	4
partial gene	4
seven field	4
different regions	4
high nucleotide	4
eastern china	4
vertical transmission	4
viral infectivity	4
sample genealogy	4
recent korean	4
human giv	4
stop codon	4
sylvatic strains	4
four isolates	4
gene segments	4
encephalitis vaccines	4
van dijk	4
entropy value	4
isolate names	4
viral shedding	4
region encompassing	4
reflect bootstrap	4
ten polish	4
hoping hospital	4
strain giv	4
diarrheic feces	4
interferon production	4
neutralization assay	4
fekov sequences	4
different methods	4
changes may	4
dna analyzer	4
branch point	4
invitrogen ltd	4
chinese qx	4
sensu lato	4
genomic characterisation	4
full length	4
person transmission	4
forest biome	4
conformational changes	4
parsimony methods	4
beta interferon	4
gallus gallus	4
consensus level	4
virus detected	4
future research	4
rotavirus species	4
even though	4
gvi feline	4
respiratory symptoms	4
pteropus giganteus	4
genotype constellation	4
epidemic wave	4
days post	4
human bufavirus	4
coronavirus hku	4
south east	4
will provide	4
protein orf	4
one sample	4
naturally occurring	4
neutralization assays	4
hr domain	4
duck hepatitis	4
european bats	4
aa sequences	4
maximum immunogenicity	4
geneious software	4
alignment showed	4
results revealed	4
five different	4
vaccine virus	4
nov genome	4
rrs sequences	4
bkov strain	4
molecular sequences	4
sera titrated	4
taq polymerase	4
mass type	4
natural environments	4
relatively low	4
molecular epidemiological	4
epitope loaded	4
environmental parameters	4
embryonated chicken	4
rectal swabs	4
miseq reagent	4
novs genetically	4
protein contained	4
genetic evolution	4
terminal domain	4
ongoing adaptation	4
unique evolutionary	4
random hexamers	4
massachusetts serotype	4
apparently new	4
close contact	4
antigenic variation	4
constant population	4
host receptor	4
vaccine peptide	4
molecular mechanisms	4
swedish crcov	4
aedes aegypti	4
like rva	4
medical conditions	4
friendly biological	4
antigenicity scores	4
autumnal prevalence	4
uk software	4
sequence alignments	4
iedb server	4
shaping codon	4
zoonotic potential	4
viral attachment	4
highest identity	4
heterochronous data	4
structure elements	4
visualized using	4
web server	4
mutations involved	4
index values	4
cytopathic effect	4
eight sequences	4
ev virus	4
evolutionary changes	4
different hosts	4
search tool	4
cleavage sites	4
highest identities	4
kb fragment	4
borrelia sp	4
west bengal	4
containing insertions	4
disease control	4
masked palm	4
may help	4
case fatality	4
neighbor base	4
statistical support	4
detailed comparative	4
zoonotic spillover	4
assay targeting	4
pcr reactions	4
genetic polymorphism	4
settlements cover	4
methods used	4
coronavirus pathogenesis	4
heptad repeat	4
likelihood trees	4
three groups	4
specific rt	4
first sars	4
infected individual	4
also reported	4
evolutionary distance	4
polish variants	4
breakpoint sites	4
evolving viruses	4
urbanized areas	4
ethnic groups	4
genomic organization	4
also used	4
branch reflect	4
natural hosts	4
healthy cats	4
chemokine genes	4
study using	4
aa insertion	4
sequences located	4
strongly associated	4
randomly selected	4
group antigens	4
prepared using	4
alignment using	4
genomic surveillance	4
kobuvirus genome	4
human rotavirus	4
technical assistance	4
ibv serotypes	4
democratic republic	4
free water	4
viral polymerase	4
distress syndrome	4
structure prediction	4
recombinant strains	4
fecal viral	4
canine gvi	4
beta barrel	4
software suite	4
year period	4
new epidemic	4
genomics workbench	4
including humans	4
sars cases	4
causative agent	4
family flaviviridae	4
acid positions	4
proteins also	4
death toll	4
immune status	4
amplified products	4
complete orf	4
aa long	4
genetic diversities	4
ev coding	4
genetically similar	4
plot analysis	4
shift protein	4
data associated	4
alignment software	4
one deletion	4
tree topology	4
complete bkov	4
reported sequences	4
birds coronavirus	4
ln china	4
bkov positive	4
viruses may	4
sequence comparison	4
coalescent process	4
dna samples	4
fecal sample	4
reactive primers	4
windows nt	4
basic local	4
hiv aids	4
novs strains	4
antigenically related	4
host gene	4
gansu province	4
personal relationships	4
furin cleavage	4
seven epitopes	4
local alignment	4
compositional constraints	4
descending order	4
web version	4
probable bat	4
gene showed	4
highest hydrophilicity	4
research council	4
relative genetic	4
factors may	4
rrs fragments	4
using clustalw	4
biological functions	4
lopinavir ritonavir	4
growth factor	4
similarity plot	4
ancestral locations	4
potential novel	4
asymptomatic animals	4
animal health	4
strains may	4
diverse trna	4
previous endemic	4
stochastic sir	4
stochastic models	4
strain sa	4
bootstrap value	4
may increase	4
cause severe	4
genus flavivirus	4
fidelity dna	4
clinical trials	4
human ifn	4
bat genera	4
angiotensin converting	4
significantly lower	4
hexon protein	4
primers targeting	4
virus variants	4
descriptive study	4
consensus sequences	4
one isolate	4
orf orf	4
control strategies	4
base preferences	4
novel parvovirus	4
strains based	4
pathogenic strains	4
female balb	4
iav prevalence	4
new host	4
nasopharyngeal swabs	4
enteric coronavirus	4
virus dynamics	4
zhangye city	4
feline enteric	4
formed two	4
rab shared	4
blot analysis	4
variation within	4
asymptomatic cats	4
virus species	4
animal novs	4
rdrp fragment	4
prefusion conformation	4
rna folding	4
mutagenesis studies	4
swedish national	4
nile virus	4
alignment containing	4
tumor necrosis	4
virus vp	4
strong binders	4
cov may	4
flab sequences	4
one step	4
human settlements	4
flying foxes	4
pcr assays	4
help us	4
many studies	4
competing interests	4
data collection	4
rna interference	4
disease progression	4
poultry industry	4
human ifng	4
fcv strains	4
based diagnostics	4
taq dna	4
genetic sequence	4
recombination among	4
pedv isolates	4
family reoviridae	4
nonstructural protein	4
primary solid	4
coronavirus genomes	4
immune cells	4
wuhan city	4
key factor	4
three times	4
high sequence	4
strain rva	4
relative synonymous	4
complete deletion	4
single introduction	4
urban mallards	4
canine strains	4
sequencing reads	4
coronavirus pneumonia	4
jv i	4
qiagen gmbh	4
ifn production	4
cytokine storm	4
irrigated cultures	3
tested negative	3
rt master	3
host reservoir	3
real time	3
repeat region	3
mutational bias	3
coronavirus outbreak	3
novel norovirus	3
sea level	3
additional studies	3
syndrome coronaviruses	3
continued surveillance	3
avian rna	3
municipal hoping	3
may involve	3
epidemiological dynamics	3
high rates	3
ribosomal rna	3
massachusetts pathogenic	3
cells expressing	3
neutralizing antibody	3
named sars	3
widespread distribution	3
immunogenic peptide	3
sigma protein	3
spatial structure	3
distinct clades	3
vp genotype	3
analysis shows	3
chinese provinces	3
additional primers	3
may cause	3
interspecies jumping	3
previously unknown	3
pathogenic avian	3
membrane glycoprotein	3
epitope conservancy	3
recombination using	3
report showed	3
encoding regions	3
analyses performed	3
formal analysis	3
length orf	3
infect mammals	3
epidemic sequences	3
comparative study	3
new york	3
viral adaptation	3
proinflammatory cytokines	3
comparative method	3
two types	3
diverse sarsr	3
underlying mechanism	3
potential risk	3
transcription factor	3
major groups	3
viral outbreaks	3
fcv evolution	3
functional receptor	3
virus caused	3
substitution matrices	3
worldwide distribution	3
different organs	3
sangon biotech	3
strain nomenclature	3
lsc i	3
coronavirus study	3
variation analysis	3
two non	3
human interspecies	3
findings indicate	3
selective pressures	3
slightly different	3
human aiv	3
fatality rate	3
global sars	3
highly similar	3
viral evolutionary	3
population growth	3
ibv genomes	3
central nervous	3
time reversible	3
cell membrane	3
geographic clustering	3
forward primer	3
main focus	3
wild waterfowl	3
genetic material	3
housing complex	3
clinical symptoms	3
kinetics selection	3
ii coronaviruses	3
health emergency	3
research foundation	3
genotype frequencies	3
transmission potential	3
virus origins	3
nov spontaneous	3
norovirus gii	3
pan troglodytes	3
bigger datasets	3
bat population	3
template rna	3
population density	3
anthropized environments	3
transfected cells	3
poultry farming	3
several studies	3
grassland cover	3
new respiratory	3
brownian diffusion	3
single gene	3
potential peptide	3
polymerase complex	3
envelope glycoprotein	3
genomic region	3
genus betacoronavirus	3
one non	3
mammalian orthoreoviruses	3
based vaccine	3
ha segment	3
reverse primers	3
nucleotide fragment	3
must fit	3
economic losses	3
roc cdc	3
neutral evolution	3
changes produced	3
using sanger	3
rhesus macaque	3
sanger method	3
missense mutation	3
bp fragment	3
orf finder	3
two axes	3
four serotypes	3
nucleotide archive	3
spatial continuum	3
gisaid database	3
gastroenteritis outbreak	3
field strain	3
strains using	3
vero cells	3
cell cultures	3
major genotype	3
cause disease	3
homo sapiens	3
greater mekong	3
viruses sequenced	3
horseshoe bat	3
specific antibodies	3
encoding region	3
sequence comparisons	3
expression level	3
immunodominant region	3
diarrhoea virus	3
related species	3
protein expression	3
lineage contained	3
peptide segments	3
targeted protein	3
biological function	3
diseased tissues	3
two residues	3
diagnostic tools	3
saharan africa	3
sra dataset	3
coalescent framework	3
causes severe	3
identical sequences	3
contagious disease	3
analysis found	3
nucleotide insertion	3
virus host	3
coronavirus proteins	3
infectious agents	3
study conducted	3
enteritis signs	3
easy vector	3
three reemerging	3
primer sequence	3
especially among	3
similarity index	3
diarrheic cats	3
exponentially distributed	3
enteric viruses	3
putative recombination	3
human settlement	3
rscu values	3
genes revealed	3
taipei municipal	3
viruses associated	3
novel canine	3
using different	3
single stranded	3
novel bkov	3
likely involves	3
clinically proven	3
ethidium bromide	3
nov gvi	3
virus genotype	3
genome contains	3
evidence suggests	3
new member	3
spike receptor	3
consecutive seasons	3
molecular markers	3
epidemiological parameters	3
temperate regions	3
phylogenetic relationship	3
bats middle	3
replications using	3
orf overlap	3
multivariate analysis	3
genetic information	3
unidirectional neutralization	3
suppress host	3
codon contents	3
control measures	3
previous korean	3
binding properties	3
findings provide	3
among humans	3
science foundation	3
variant strains	3
proven protease	3
pressure analysis	3
coalescent theory	3
tc per	3
fastq files	3
wild short	3
widely distributed	3
codon preference	3
em structure	3
mer peptides	3
like protease	3
like vaccine	3
increased contact	3
coalescent approaches	3
sequences carrying	3
hrsv subgroup	3
dog gvi	3
urban environment	3
limited genetic	3
control plasmid	3
rflp method	3
dabbling ducks	3
available genomes	3
literature review	3
large phylogenies	3
multiple mutations	3
ab polyprotein	3
sliding window	3
three consecutive	3
tumor types	3
sequences support	3
hospitalizations among	3
cellular receptor	3
mainland china	3
using axyprep	3
two main	3
recovery phase	3
direct evidence	3
south china	3
animal ethics	3
numbers mk	3
strain may	3
results show	3
receptor usage	3
population dynamic	3
developing countries	3
similar structures	3
feline parvovirus	3
negative stain	3
chicken farms	3
simple vector	3
using samtools	3
genus kobuvirus	3
either alone	3
interferon signaling	3
reovirus sigma	3
therapeutic development	3
million people	3
viruses detected	3
relatively high	3
time tree	3
analyzed strains	3
room temperature	3
cancer types	3
hendra virus	3
noroviruses detection	3
cell fusion	3
epitope regions	3
single virus	3
protein orfs	3
evolutionary processes	3
recombinant virus	3
parameter model	3
refractory mutational	3
giganteus bat	3
utr region	3
translated proteins	3
known bkov	3
genetic relatedness	3
epidemic areas	3
genetic sublineages	3
sequence closest	3
detection methods	3
global distribution	3
glycosylation sites	3
expression systems	3
human bocavirus	3
variable rates	3
comprised aois	3
aquatic birds	3
glycoprotein sequence	3
tissue damage	3
two groups	3
translational levels	3
plasmids pgl	3
experimentally demonstrated	3
proof coronavirus	3
kidney tissue	3
viral dsrna	3
candidate new	3
source population	3
high levels	3
megalign program	3
first detection	3
variable regions	3
branch lengths	3
using superscript	3
investigated whether	3
epidemic diseases	3
cosmopolitan genotypes	3
avian astroviruses	3
analyses based	3
three sequences	3
phylogenetic approaches	3
host shifts	3
genogroup giv	3
immunoinformatics approach	3
arg constituting	3
encoding six	3
cell responses	3
coronavirus cross	3
gov orffinder	3
prior density	3
reverse transcribed	3
adenovirus infection	3
second region	3
nosocomial infection	3
bp pcr	3
bkov detection	3
evolving infectious	3
stable cell	3
many countries	3
secondary infections	3
pars trees	3
scientific research	3
stimulating factor	3
intestinal content	3
human health	3
bp including	3
evolutionary origin	3
chagasic cardiomyopathy	3
different lengths	3
recent outbreaks	3
mice inoculated	3
tuning translation	3
nov rna	3
bat diversity	3
vp nucleotide	3
high elevation	3
different bat	3
dipeptidyl peptidase	3
gardens housing	3
health policies	3
aa protein	3
vaccinated chickens	3
substantial evidence	3
influenza pandemic	3
diversity among	3
korean field	3
mice infected	3
geographic locations	3
cov genome	3
first identification	3
viral strain	3
design functional	3
end illumina	3
coronavirus sub	3
ecg alterations	3
identified homoplasies	3
variable region	3
freshly deposited	3
two major	3
rna sequences	3
grassland areas	3
chosen preferentially	3
acid replacements	3
bioinformatics analysis	3
analysis indicated	3
wt arg	3
positive sample	3
omics analysis	3
viral particles	3
hotspot sequences	3
evolutionary studies	3
host exists	3
underlying diseases	3
alignment editor	3
network protocol	3
tract infection	3
guano farms	3
viral genes	3
mega software	3
secondary structures	3
possible transmission	3
strains revealed	3
national park	3
sequences respectively	3
remaining flab	3
one virus	3
ibv field	3
still needs	3
made using	3
winter months	3
vaccine candidate	3
gene products	3
second axis	3
small sample	3
th dpi	3
evidence supporting	3
ancestral origin	3
underlying medical	3
vital role	3
profiles retrieved	3
one sequence	3
parsimony tree	3
cell proliferation	3
viral sequences	3
traditional vaccines	3
hospitalized patients	3
diseased chickens	3
spf chicken	3
conserved sequence	3
first step	3
high homology	3
nearly complete	3
putative non	3
third index	3
santa clara	3
varied according	3
infected cell	3
two ibv	3
mrna expression	3
study clustered	3
natural science	3
data set	3
cellular machinery	3
immune failure	3
antigenically distinct	3
coronavirus kb	3
insertion site	3
various genotypes	3
mostly deletions	3
multiple times	3
substitution parameters	3
three non	3
nsp suppresses	3
negative control	3
western analysis	3
viral species	3
first case	3
fc clusters	3
hydropathy index	3
aminoacid sequences	3
high identity	3
study provides	3
comparative studies	3
saudi arabia	3
ncov spike	3
epitope position	3
strains except	3
codon usages	3
ribosomal frameshift	3
using mafft	3
complete nucleotide	3
strict clock	3
group coronavirus	3
tc aus	3
neutralizing titer	3
hemorrhagic fever	3
global af	3
mixed models	3
vp lineages	3
four strains	3
translationally cleaved	3
supplementary tables	3
outer capsid	3
protein production	3
nt similarity	3
infected seroconverters	3
internal nodes	3
relatedness values	3
ifn induction	3
close evolutionary	3
pathogen free	3
ifng genotype	3
host factors	3
homogeneous substitution	3
mrv strain	3
key roles	3
bats isolation	3
limited sequences	3
coronavirus sars	3
cipres science	3
using illumina	3
implicated cytokine	3
two chinese	3
immune escape	3
three independent	3
carrying large	3
infection cycle	3
aroma values	3
vertebrate cell	3
group coronaviruses	3
informed consent	3
tioman island	3
protein plays	3
siv lineages	3
polymorphism may	3
bioedit software	3
receptor ace	3
statistical phylogeography	3
antigenic resemblance	3
cluster tree	3
regulatory factor	3
computer program	3
multiple countries	3
deduced aa	3
complete sequences	3
analysis suggested	3
lasergene software	3
temporal structure	3
mutated positions	3
pathogenicity factor	3
animal experiments	3
vitro mutagenesis	3
rotavirus classification	3
previously characterized	3
coalescent approach	3
camel blood	3
cov infected	3
synonymous substitutions	3
fetal bovine	3
long distance	3
tissues seems	3
host may	3
like receptors	3
qx strain	3
bovine serum	3
population model	3
controlled trial	3
scoring system	3
life cycle	3
genome characterization	3
aids pandemic	3
gene contained	3
identity matrix	3
using figtree	3
temporal dynamics	3
immunogenicity scores	3
another group	3
selection plays	3
composition constraints	3
avian species	3
insectivorous bats	3
negative sera	3
renilla luciferase	3
also displayed	3
ita displayed	3
within orf	3
translation initiation	3
extension step	3
agricultural sciences	3
local clock	3
social distancing	3
pcr based	3
recombinant vaccinia	3
glycoprotein gene	3
genome consists	3
estimate maximum	3
codon preferences	3
excluding masked	3
relative frequencies	3
virus isolate	3
past population	3
emerging genotype	3
base region	3
method based	3
distilled water	3
causative agents	3
interferon induction	3
synonymous variant	3
host jumps	3
vaccines based	3
novel coronaviruses	3
species barrier	3
higher prevalence	3
predominant strain	3
compared using	3
constructed based	3
detectable positive	3
using geneious	3
primer sets	3
sequencing using	3
nt exhibited	3
contact network	3
software figtree	3
animal reservoirs	3
pathogenic sars	3
major cause	3
bordetella bronchiseptica	3
mhc molecules	3
rna molecule	3
ili region	3
regulates replication	3
major capsid	3
pathogenic coronaviruses	3
sylvatic cycle	3
designing sirnas	3
genes encoding	3
based population	3
nov genetic	3
type ii	3
ethical committee	3
evolution analysis	3
reovirus isolated	3
method using	3
unique mechanism	3
transmission rates	3
type genomes	3
virus titer	3
trna pool	3
swedish research	3
virus molecular	3
numbers mh	3
short read	3
missense variants	3
deduced aminoacid	3
viral proteases	3
extremely high	3
viral interaction	3
american countries	3
weak codon	3
ninth report	3
total variation	3
positive rates	3
threshold value	3
genomic positions	3
bats captured	3
infections caused	3
rotavirus isolated	3
glycoprotein genes	3
sequences deposited	3
list threat	3
epidemic diarrhoea	3
ndv infection	3
pathological changes	3
showed significant	3
regions within	3
animal diseases	3
genus leptospira	3
aa identities	3
junction region	3
ch scem	3
pet dog	3
spatial distribution	3
mutations produced	3
attenuated vaccine	3
previously shown	3
strains formed	3
matched non	3
virus characterization	3
protective immunity	3
mediated editing	3
eight normal	3
bioinformatic tools	3
mutational system	3
science gateway	3
highest similarity	3
pathogenic role	3
structural basis	3
viral metagenomics	3
luciferase reporter	3
animal ethical	3
adaptation index	3
including yunnan	3
sequences indicated	3
binary matrix	3
preferential selection	3
epidemic modeling	3
wild migrating	3
cell linear	3
live vaccine	3
ten strains	3
sensu stricto	3
virus circulating	3
distinct ibv	3
us pedv	3
poultry population	3
us protein	3
primer pairs	3
severe cases	3
genes coding	3
positive correlation	3
evade host	3
inferred age	3
barr virus	3
natural reservoir	3
recombinant sequences	3
involves several	3
vertebrate cells	3
major factors	3
highly prevalent	3
intersubtype recombination	3
china including	3
major determinant	3
strains cluster	3
observed near	3
closed sir	3