trigram

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

trigram	frequency
infectious bronchitis virus	145
in this study	114
acute respiratory syndrome	88
severe acute respiratory	87
of infectious bronchitis	77
based on the	74
of the s	73
analysis of the	67
respiratory syndrome coronavirus	64
codon usage bias	62
the presence of	56
of the virus	55
j o u	54
u r n	54
n a l	54
o u r	54
the s gene	54
r n a	54
closely related to	53
avian infectious bronchitis	49
p r o	48
o o f	48
p r e	48
r o o	48
genet evol doi	48
l p r	48
infect genet evol	48
a l p	48
synonymous codon usage	46
according to the	46
the codon usage	46
in order to	45
in the s	44
the number of	44
as well as	44
the s subunit	43
one of the	42
genetic diversity of	42
respiratory syncytial virus	39
codon usage pattern	38
sequences of the	38
phylogenetic analysis of	38
ck ch lhlj	38
and ck ch	37
a total of	37
of codon usage	37
characterization of a	36
genetics and evolution	35
related to the	35
the present study	33
martella et al	32
the phylogenetic tree	31
molecular characterization of	31
of a novel	31
the complete genome	31
east respiratory syndrome	30
of the sars	30
middle east respiratory	30
of avian infectious	30
codon usage in	29
the vp gene	29
influenza a virus	29
li et al	29
of the genome	29
the evolution of	29
the development of	28
hepatitis c virus	28
the s protein	27
the emergence of	27
codon usage of	27
and amino acid	26
were collected from	26
shown in fig	26
due to the	25
liu et al	25
can be found	25
bronchitis virus in	25
the genetic diversity	24
ch lhlj vii	24
s coding region	24
s and s	24
this study was	23
end of the	23
was used to	23
of severe acute	23
region of the	23
wang et al	23
of ns protein	23
a and b	23
to determine the	22
the distribution of	22
article can be	22
compared to the	22
the reemerging korean	22
showed that the	22
this article can	22
the spike protein	21
lu et al	21
found to be	21
rna was extracted	21
usage pattern of	21
in the present	21
were used to	20
was extracted from	20
were obtained from	20
ck sudan ar	20
usage bias of	20
identified in the	20
human respiratory syncytial	20
genome sequences of	20
most of the	20
o f journal	19
multiple sequence alignment	19
f journal pre	19
strain ck ch	19
were found to	19
as shown in	19
of the vp	19
the results of	19
deposited in genbank	19
sequence analysis of	19
open reading frame	19
and evolution of	19
the s and	19
the prevalence of	19
nucleotide and amino	19
of this virus	19
complete genome sequences	19
revealed that the	19
molecular epidemiology of	19
of a new	18
we found that	18
found online at	18
be found online	18
was found to	18
martino et al	18
to understand the	18
to this article	18
the role of	18
lacroix et al	18
and characterization of	18
obtained from the	18
in south korea	18
data to this	18
in the vp	18
supplementary data to	18
characterization of the	18
di martino et	18
open reading frames	18
in wild birds	17
was supported by	17
zhou et al	17
in recent years	17
the amino acid	17
of the hrsv	17
s and n	17
were included in	17
of synonymous codon	17
the genome of	17
amino acid sequences	17
of the total	17
pcr products were	17
in the same	17
vp and vp	17
of these viruses	17
was isolated from	17
large number of	17
were identified in	17
analysis based on	17
a number of	16
to that of	16
the sars coronavirus	16
located in the	16
found in the	16
most closely related	16
cd t cells	16
ck ch scyb	16
to identify the	16
codon usage patterns	16
in this work	16
the sequence of	16
woo et al	16
a phylogenetic tree	16
belonging to the	16
world health organization	16
and n proteins	16
been detected in	16
it has been	16
polish ibv strains	16
wille et al	16
that of the	16
the origin of	16
be used to	16
japanese encephalitis virus	15
the maximum likelihood	15
nsp proteins of	15
this is the	15
of novel coronavirus	15
found that the	15
reemerging korean pedv	15
of the reemerging	15
sequence of the	15
is the first	15
of the g	15
this work was	15
of this study	15
can be used	15
of the host	14
of the human	14
the lack of	14
a novel coronavirus	14
associated with the	14
the host cell	14
phylogenetic tree was	14
isolated from a	14
were isolated from	14
of hepatitis c	14
the result of	14
genome sequence of	14
belonged to the	14
the time of	14
analysis showed that	14
infectious bronchitis coronavirus	14
have been reported	14
are shown in	14
drummond et al	14
the analysis of	14
the relationship between	14
genome of the	14
human immunodeficiency virus	14
strains ck ch	14
were positive for	14
of the ibv	14
detected in the	14
were closely related	14
structure of the	14
responsible for the	14
protein of sars	14
of the spike	13
positive samples were	13
on the s	13
the end of	13
chen et al	13
ck ch lnm	13
the g protein	13
the s glycoprotein	13
of the population	13
regions of the	13
of the novel	13
observed in the	13
of human respiratory	13
jz and cc	13
of the orf	13
the synonymous codon	13
all of the	13
dependent rna polymerase	13
korean pedv strains	13
the orf a	13
was performed using	13
the frequency of	13
to investigate the	13
in the phylogenetic	13
of the four	13
analysis of codon	13
as a result	13
amino acid identities	13
with those of	13
genetic diversity and	13
of the viral	13
samples were collected	13
the phylogenetic analysis	13
canine respiratory coronavirus	13
evolutionary genetics analysis	13
have been identified	13
shown to be	13
huang et al	13
used as a	13
of the phylogenetic	13
molecular evolutionary genetics	13
is associated with	13
shown in table	13
matthijnssens et al	13
were subjected to	13
infectious bronchitis viruses	13
the existence of	13
evolution of the	13
phylogenetic analysis based	12
a g p	12
the samples were	12
are associated with	12
parts of the	12
been reported in	12
xu et al	12
the s coding	12
role in the	12
isolation and characterization	12
group i coronavirus	12
understanding of the	12
in the united	12
and molecular characterization	12
of the n	12
identification of a	12
ck ch ldl	12
vp gene of	12
a large number	12
nucleotide sequences of	12
amino acid changes	12
similar to the	12
ns and ns	12
tree was constructed	12
a result of	12
the united states	12
was found in	12
in the orf	12
the majority of	12
chu et al	12
mutations in the	12
were found in	12
changes in the	12
the population size	12
origin of the	12
natural selection from	12
s gene of	12
pattern of ev	12
amino acid sequence	12
in southwestern china	12
thermo fisher scientific	11
g p rotavirus	11
the authors declare	11
results of the	11
a new coronavirus	11
were detected in	11
ibv strains were	11
d g mutation	11
characteristics of the	11
suggest that the	11
analysis of a	11
a previous study	11
higher than that	11
the effects of	11
of borrelia burgdorferi	11
complete genome of	11
balb c mice	11
in accordance with	11
analysis revealed that	11
the effect of	11
be related to	11
a role in	11
an outbreak of	11
around the world	11
to assess the	11
the virus to	11
the nucleotide sequences	11
the sequences of	11
sequences from the	11
aliphatic amino acids	11
of b virus	11
age of the	11
part of the	11
supported by the	11
work was supported	11
tree based on	11
coding sequence of	11
for min at	11
on the surface	11
for the first	11
human influenza a	11
zhang et al	11
this study were	11
the genbank database	11
in southern china	11
the extent of	11
spike protein of	11
phylogenetic trees were	11
online at https	11
of japanese encephalitis	11
viral rna was	11
were located in	11
porcine epidemic diarrhea	11
b and ns	11
was detected in	11
to those of	11
in the genome	11
a final extension	11
the novel coronavirus	11
lemey et al	11
in the spike	11
hu et al	11
of the world	11
genetic characterization of	11
overall codon usage	11
amino acid composition	11
with that of	11
s rrna gene	11
single nucleotide polymorphism	11
some of the	11
the use of	11
and stored at	10
coding sequences of	10
in northeast china	10
the first time	10
deletion and insertion	10
with acute respiratory	10
considered to be	10
of chagas disease	10
important role in	10
the pcr products	10
genbank accession numbers	10
of sars coronavirus	10
to each other	10
on the other	10
the n gene	10
was carried out	10
and avian coronaviruses	10
was used for	10
the g gene	10
genbank accession number	10
those of the	10
to better understand	10
polymerase chain reaction	10
the sequences were	10
tamura et al	10
ck ch scdy	10
in our study	10
as previously described	10
lau et al	10
were used for	10
member of the	10
coronavirus infectious bronchitis	10
analysis of synonymous	10
the characteristics of	10
corman et al	10
the first report	10
the complete polyprotein	10
of influenza a	10
the possibility of	10
kamitani et al	10
with the same	10
and phylogenetic analysis	10
was used as	10
in ns protein	10
than that of	10
gene source of	10
yang et al	10
to be the	10
reuter et al	10
that there is	10
host innate immunity	10
indicate that the	10
the surface of	10
the risk of	10
in south america	10
is shown in	10
of the tree	10
prevalence of the	10
ns b and	10
members of the	10
the spread of	10
as the gene	10
the other hand	10
pathogenic leptospira spp	10
and nsp genes	10
the detection of	10
an important role	10
of the two	10
were performed using	10
is the most	10
the rate of	10
a member of	10
the dynamics of	10
the importance of	10
the whole coding	10
g p rva	10
the whole genome	10
comparative analysis of	10
the nucleotide and	10
of the disease	10
the evolution and	10
of the covid	10
wu et al	10
proteins of sars	10
h n influenza	10
the gene source	10
in codon usage	10
in addition to	10
obtained in this	10
the virus in	10
and identification of	10
play a role	10
was performed by	10
in terms of	10
in the uk	10
of the ifng	10
the s rrna	10
s subunit gene	10
in the first	10
coronaviruses as the	10
e and hcov	10
and vp genes	9
diversity of sars	9
of the coronavirus	9
for the development	9
respiratory disease in	9
to estimate the	9
and ecological processes	9
likely to be	9
resulting in a	9
of d g	9
fecal samples were	9
of dengue virus	9
of the complete	9
in the sars	9
more closely related	9
the n protein	9
it is important	9
coronaviruses in the	9
of borrelia spp	9
be involved in	9
selection from host	9
the circulation of	9
to the same	9
in humans and	9
the transmission of	9
available in the	9
are required to	9
and a final	9
the epidemiology of	9
humans and animals	9
of the most	9
g and g	9
the emergence and	9
be associated with	9
with the highest	9
whole coding sequence	9
within the s	9
a combination of	9
newcastle disease virus	9
and analysis of	9
with respect to	9
the genomes of	9
strains in the	9
length of the	9
to amplify the	9
tolf et al	9
is responsible for	9
is a major	9
indicated that the	9
i coronavirus nsp	9
chua et al	9
may not be	9
strains have been	9
phylogenetic tree of	9
in the field	9
it may be	9
virus infection in	9
has also been	9
the nsp proteins	9
has been reported	9
epidemic diarrhea virus	9
included in the	9
was constructed using	9
were carried out	9
to be a	9
vasilakis et al	9
first identified in	9
isolated from the	9
and natural selection	9
present in the	9
been shown to	9
c and g	9
may be involved	9
phylogenetic tree based	9
of the genetic	9
with the chinese	9
differences in the	9
of amino acid	9
there is a	9
global spread of	9
and in vivo	9
ck ch cqkx	9
in the genbank	9
drexler et al	9
amino acid residues	9
in the host	9
amino acid identity	9
the vp protein	9
usage bias in	9
stranded rna viruses	9
strains isolated from	9
immunodeficiency virus type	9
cell epitopes were	9
is one of	9
international committee on	9
orf a b	9
which may be	9
in the genus	9
the on genotype	9
and mouth disease	9
of the us	9
the occurrence of	9
the most variable	9
used in this	9
to obtain a	8
this study are	8
the ecology of	8
were higher than	8
detection and molecular	8
emerging infectious diseases	8
the selection of	8
related to human	8
has not been	8
coronavirus nsp proteins	8
genetic characteristics of	8
were analyzed using	8
and ns proteins	8
a review of	8
of a virus	8
of pathogenic leptospira	8
analysis of infectious	8
usage of the	8
the degree of	8
eshaghi et al	8
genomic characterization of	8
national veterinary institute	8
c and a	8
spread of the	8
at the end	8
need to be	8
and evaluation of	8
complete polyprotein gene	8
as a potential	8
to evaluate the	8
the pattern of	8
was discovered in	8
distribution of the	8
national center for	8
positively selected sites	8
in the order	8
in dogs with	8
the course of	8
constructed using the	8
insight into the	8
samples collected from	8
major role in	8
sequences and the	8
in the g	8
trypanosoma cruzi infection	8
was determined by	8
recent common ancestor	8
lee et al	8
genomes of the	8
as described in	8
were aligned using	8
du et al	8
was performed in	8
were submitted to	8
m and m	8
was performed with	8
mesquita et al	8
have been detected	8
strains identified in	8
to explore the	8
complete genome sequence	8
the pathogenesis of	8
committee on taxonomy	8
on the complete	8
martin et al	8
to the canine	8
of bats and	8
belongs to the	8
of the genus	8
the most frequent	8
sequence of ev	8
strains were isolated	8
in genbank under	8
the same time	8
accession numbers are	8
of the hiv	8
canine infectious respiratory	8
associated with a	8
ck ch scms	8
maximum likelihood method	8
the middle east	8
domain of the	8
of ev and	8
on taxonomy of	8
of the b	8
gene sequences of	8
better understand the	8
first report of	8
the overall codon	8
the introduction of	8
and s subunits	8
the presence and	8
was identified in	8
molecular characteristics of	8
detected in a	8
in the n	8
size of the	8
results suggest that	8
of polish ibv	8
the age of	8
cell epitopes of	8
taxonomy of viruses	8
of group i	8
the interaction of	8
infectious respiratory disease	8
center for biotechnology	8
results showed that	8
were observed in	8
sequences of ev	8
patients infected with	8
the international committee	8
the orf gene	8
as compared to	8
with diarrhea in	8
in the middle	8
zou et al	8
avian influenza virus	8
amino acid substitutions	8
bronchitis virus from	8
the tree was	8
urban and sylvatic	8
p rotavirus strain	8
of ev strains	8
codon usage is	8
lnm and ck	8
as part of	8
n proteins of	8
codon usage and	8
were deposited in	8
zhao et al	8
and epidemiology of	8
of ck ch	8
morbidity and mortality	8
ch lnm and	8
calisher et al	8
the vp and	8
a simple method	8
products were purified	7
collected from the	7
the absence of	7
compared with the	7
demonstrated that the	7
the interaction between	7
g mutation in	7
fekov reference strains	7
of the synonymous	7
decaro et al	7
of e protein	7
peptide vaccine formulation	7
in contrast to	7
that the b	7
in the alignment	7
of the h	7
the entire genome	7
protein is a	7
human and animal	7
s protein of	7
of the three	7
orf gene of	7
shaping the codon	7
tc chn sccd	7
cui et al	7
sites of the	7
in indian patients	7
su et al	7
difference in the	7
field strains and	7
of which were	7
on the full	7
in the case	7
gammacoronavirus and deltacoronavirus	7
coding region of	7
is based on	7
the ability to	7
is found in	7
drug and vaccine	7
and their hosts	7
an increase in	7
diversity of the	7
reported to be	7
studies are required	7
novs have been	7
the highest nucleotide	7
the length of	7
of bats in	7
was the most	7
major hexon variants	7
roles in the	7
the generation of	7
in the us	7
the canine strain	7
that have been	7
reemerging korean strains	7
the us strains	7
hewson et al	7
shi et al	7
emergence of a	7
in the emergence	7
may be related	7
orf encodes a	7
cavanagh et al	7
of leptospira spp	7
was closely related	7
the diversity of	7
caddy et al	7
of recombination in	7
of the codon	7
emergence of new	7
was obtained from	7
sequences were aligned	7
for the whole	7
has been used	7
the fact that	7
with each other	7
orf and orf	7
the world health	7
have been deposited	7
host protein synthesis	7
the ace receptor	7
a frame shift	7
partial d gene	7
different host species	7
of fecal samples	7
maximum likelihood phylogenetic	7
carried out using	7
rna recombination in	7
could not be	7
and the complete	7
s subunit of	7
strains isolated in	7
performed using the	7
chan et al	7
evidence for the	7
analysis was performed	7
sequence identity with	7
of the whole	7
purified core protein	7
blicharz et al	7
and pathogenicity of	7
with the canine	7
the breakpoint site	7
is known to	7
and in the	7
complete vp gene	7
clustered with the	7
in cats in	7
valastro et al	7
of bat sarsr	7
phylogenetic analysis was	7
in southeast asia	7
in the rok	7
impact on the	7
molecular evolution of	7
also found that	7
been found in	7
belong to the	7
have also been	7
of the capsid	7
depending on the	7
are the most	7
insights into the	7
chinese horseshoe bats	7
presence and absence	7
samples were identified	7
protein the epitope	7
data not shown	7
of kobuvirus in	7
been deposited in	7
followed by the	7
were identified as	7
we also found	7
did not show	7
were assembled using	7
pcr was performed	7
based on a	7
virus and the	7
information on the	7
takano et al	7
and that of	7
of vaccine strains	7
for biotechnology information	7
distantly related to	7
in which the	7
values for the	7
of amino acids	7
the influenza a	7
bayesian phylogenetic inference	7
reported that the	7
the virus was	7
to the s	7
results indicate that	7
crcov and bcov	7
of human coronavirus	7
authors declare that	7
of avian coronavirus	7
lan et al	7
events in the	7
was extracted using	7
identified in this	7
located on the	7
diagnostics and vaccines	7
is necessary to	7
zheng et al	7
have been isolated	7
which is the	7
the secondary structure	7
to our knowledge	7
erles et al	7
of canine respiratory	7
infectious cdna clone	7
in the human	7
the viral genome	7
recombination in the	7
significant difference in	7
found to possess	7
of the strains	7
proteins of group	7
calculated using the	7
of human influenza	7
evolutionary and ecological	7
of rp patients	7
we analyzed the	7
we investigated the	7
identified as a	7
in domestic cats	7
in europe and	7
in the lung	7
of the sequences	7
foot and mouth	7
margalef et al	7
chagas disease in	7
with the host	7
a better understanding	7
are known to	7
these results suggest	7
tree of the	7
generated in this	7
a major role	7
of the alignment	7
using the maximum	7
complete genomes of	7
and orf b	7
cambodia and lao	7
peptide vaccine against	7
due to a	7
and the number	7
the most recent	7
nucleotide identity with	7
the accession numbers	7
and genetic characterization	7
dogs and cats	7
the complete vp	7
online at http	7
the source of	7
the e protein	7
most similar to	6
phylogenetic analysis showed	6
is important to	6
the difference in	6
cai values for	6
i e r	6
coronavirus associated with	6
final extension at	6
of the national	6
w w w	6
value of each	6
identified using the	6
synonymous in the	6
in this context	6
wide range of	6
a b gene	6
promkuntod et al	6
evolution j o	6
o m l	6
than those of	6
genbank under the	6
and lao pdr	6
genomic analysis of	6
is likely to	6
there are no	6
c o m	6
interpretation of the	6
more than one	6
in escherichia coli	6
and formed a	6
were the most	6
t a polymorphism	6
activation of the	6
between urban and	6
reverse vaccinology approach	6
the four ibv	6
the mutation points	6
were identified from	6
and the s	6
be considered as	6
l s e	6
has been shown	6
strains belonging to	6
clustered together with	6
of emerging viruses	6
of canine parvovirus	6
whole genome sequence	6
to the host	6
the case of	6
be used as	6
in poultry and	6
c and d	6
by using the	6
virus with a	6
for these viruses	6
h o m	6
the immune system	6
disease in china	6
be able to	6
were separated by	6
result of a	6
and pathogenesis of	6
the association between	6
a variety of	6
the isolation of	6
of rapidly evolving	6
at the nucleotide	6
is the major	6
and vaccine development	6
be infected by	6
were used as	6
a set of	6
kobuvirus in cats	6
hypervariable region of	6
previous studies have	6
fecal samples from	6
and social factors	6
of middle east	6
viruses such as	6
clinical characteristics of	6
from patients with	6
with a prevalence	6
mouth disease virus	6
there is no	6
s and gc	6
group i coronaviruses	6
the corresponding amino	6
m e e	6
identity with the	6
in the following	6
from southwestern china	6
kumar et al	6
e l s	6
similar to that	6
of the rna	6
could be used	6
of human sars	6
for further analysis	6
in lao pdr	6
of the overall	6
we found a	6
of canine norovirus	6
presence of a	6
canine parvovirus type	6
h and h	6
of the first	6
vaccine strain h	6
we evaluated the	6
pathogenicity of a	6
for detection of	6
singh et al	6
molecular epidemiology and	6
is known about	6
m e p	6
the rest of	6
showed the presence	6
sequence alignment and	6
c a t	6
of ibv and	6
in the population	6
displayed the highest	6
the national center	6
the activation of	6
avian coronavirus infectious	6
sequences of borrelia	6
we have also	6
chinese fekov strain	6
ck ch scmy	6
alignment of the	6
genome analysis of	6
of cd t	6
of rna viruses	6
accordance with the	6
a recombination event	6
consistent with the	6
epitopes were identified	6
that natural selection	6
chain monte carlo	6
from the analysis	6
of prm protein	6
the immune response	6
ifng t a	6
vitro and in	6
usage pattern and	6
with severe acute	6
yet to be	6
most recent common	6
diversity of ev	6
phan et al	6
using the neighbour	6
group a rotavirus	6
more similar to	6
of mutations in	6
strand cdna synthesis	6
bayesian inference of	6
markov chain monte	6
sun et al	6
nsp and nsp	6
and evolution j	6
four ibv strains	6
usage patterns of	6
have not been	6
in amino acid	6
nucleotide substitutions per	6
a collection of	6
of the epidemic	6
the vaccine strain	6
national institute of	6
avian coronaviruses in	6
close to the	6
a g e	6
l h o	6
gel extraction kit	6
outbreak associated with	6
the fecal samples	6
further studies are	6
e e g	6
and emergence of	6
in the distribution	6
of genetic diversity	6
cho et al	6
were generated using	6
serotype of infectious	6
that the s	6
analyzed using the	6
on the genetic	6
because of the	6
of the family	6
c for s	6
in a study	6
t e m	6
aliphatic amino acid	6
the h n	6
rna viruses in	6
genetics analysis version	6
based peptide vaccine	6
been identified in	6
better understanding of	6
the formation of	6
it is necessary	6
these viruses in	6
afelt et al	6
detection of norovirus	6
worobey et al	6
ck ch scls	6
the united kingdom	6
and amino acids	6
present study and	6
group a rotaviruses	6
s e v	6
the replication of	6
acute respiratory distress	6
bias of the	6
mafft multiple sequence	6
was calculated using	6
reservoir hosts of	6
to describe the	6
genetic variation in	6
signs of disease	6
a recent study	6
dengue virus type	6
of all the	6
obtained in the	6
of s and	6
and gc s	6
in guangdong province	6
pattern of the	6
the most common	6
the genome segments	6
isolation of a	6
origin and evolution	6
of the other	6
of respiratory syncytial	6
study was supported	6
cd t cell	6
sites in the	6
yamashita et al	6
but not in	6
basic reproduction ratio	6
for the presence	6
used for the	6
may play a	6
cell epitope prediction	6
of ev is	6
orf a and	6
m l o	6
virus nucleic acid	6
in clinical samples	6
with a genome	6
genetic analysis of	6
study was to	6
on genotype was	6
as described previously	6
referred to as	6
coding region sequences	6
in table s	6
the probability of	6
of the analyzed	6
o c a	6
is required to	6
with the exception	6
of the samples	6
for codon usage	6
the chinese fekov	6
trees were constructed	6
structural and functional	6
in the online	6
together with the	6
and absence of	6
o m e	6
takara bio inc	6
it is also	6
approved by the	6
authors declare no	6
they were not	6
banyai et al	6
of a qx	6
rrna gene sequences	6
with a new	6
length genomic sequences	6
a t e	6
in length and	6
the first two	6
and vaccine strains	6
alphacoronavirus and betacoronavirus	6
that can be	6
rojas et al	6
occurred in the	6
of hiv infection	6
were analyzed for	6
in silico approach	6
circulated in the	6
c viseu prt	6
the t mrca	6
p rva rabbit	6
used to amplify	6
detected in bats	6
influenza a viruses	6
based on s	6
in the c	6
recombination events in	6
e m e	6
at amino acid	6
from this study	6
poultry and other	6
amino acids in	6
such as the	6
covs have been	6
have originated from	6
studies have shown	6
to host cells	6
e p a	6
phylogenetic tree and	6
surface of the	6
and public health	6
listed in table	6
v i e	6
bronchitis virus isolates	6
of avian influenza	6
the nsp gene	6
the enc value	6
of recombination events	6
the basic reproduction	6
of a single	6
from the national	6
it is not	6
likelihood phylogenetic tree	6
was first identified	6
of coding sequences	6
of the remaining	6
genome segments of	6
common ancestor of	6
than of the	6
variability of the	6
there was no	6
the hypothesis that	6
be used in	6
in shaping the	6
p a g	6
dynamics of the	6
evolution of sars	6
little is known	6
g i d	6
for diagnostic purposes	6
fcv orf gene	6
used to analyze	6
of nipah virus	6
in the analysis	6
contribute to the	6
be explained by	6
was observed in	6
of aliphatic amino	6
and edited using	6
bayesian skyline plot	6
ibv ck sudan	6
l o c	6
was not the	6
indicates that the	6
the alignment of	6
recent years in	6
e g i	6
the bayesian skyline	6
a l h	6
for the detection	6
has been found	6
genomic sequences of	6
retrieved from the	6
e v i	6
proteins of hcov	6
in anhui province	6
emergence of the	6
nucleotide sequences were	5
sequences generated in	5
we used the	5
may be associated	5
no significant difference	5
molecular characterization and	5
in diarrhoeic cats	5
performed on the	5
infection and the	5
adaptation of sars	5
at that time	5
of highly pathogenic	5
during the course	5
walls et al	5
simian immunodeficiency virus	5
a systematic review	5
disease in a	5
compared with other	5
olsen et al	5
a separate branch	5
the history of	5
to adapt to	5
high mutation rates	5
using maximum likelihood	5
more than of	5
a close relationship	5
in an urban	5
in vitro and	5
to the genus	5
collection of fecal	5
genbank under accession	5
a h n	5
tested positive for	5
time evolution of	5
cdna synthesis kit	5
viral entry to	5
after h incubation	5
deposited in the	5
of the data	5
zhu et al	5
syndrome coronavirus in	5
it was found	5
was located at	5
other fekov strains	5
of lyme disease	5
novel mammalian and	5
of ebola virus	5
the atlantic forest	5
bonica et al	5
with b virus	5
analysis of recombination	5
is the main	5
deduced amino acid	5
of infected individuals	5
like virus in	5
nt sequence identity	5
into four genera	5
population size history	5
strains of gi	5
immune response in	5
of the infectious	5
genotypes have been	5
of nov strains	5
were calculated using	5
the ibv strains	5
and ns of	5
sars coronavirus and	5
of the pca	5
immunogenicity score of	5
garinii and b	5
east region of	5
ribosomal frame shift	5
may be important	5
isolation and identification	5
the rscu value	5
of the mass	5
not show any	5
caused by the	5
for s and	5
in a single	5
he et al	5
the potential for	5
the respiratory tract	5
the infected cells	5
the reconstruction of	5
in each aoi	5
aligned using the	5
of nucleotide substitution	5
mammalian and avian	5
of human novs	5
on the nucleotide	5
d g in	5
was present in	5
and did not	5
history of the	5
gene of fcv	5
the major hexon	5
presence of the	5
and prevalence of	5
a comparative analysis	5
had the highest	5
and it was	5
of the global	5
was reported to	5
to characterize the	5
a significant difference	5
de wit et	5
coronavirus spike protein	5
binding to the	5
crcov and crcov	5
chung et al	5
s subunit is	5
information about the	5
available on the	5
g and p	5
also detected in	5
throughout the world	5
it should be	5
of the study	5
the molecular characteristics	5
is possible that	5
important reservoir hosts	5
genus deltacoronavirus supports	5
ns protein the	5
ma et al	5
believed to be	5
jiang et al	5
interact with the	5
of borrelia species	5
different parts of	5
the negative side	5
in this region	5
was based on	5
and spread of	5
loaded peptide vaccine	5
is consistent with	5
the population history	5
the notion that	5
clinical features of	5
has been detected	5
lower respiratory tract	5
variation of the	5
to model the	5
between humans and	5
the potential of	5
were determined using	5
found only in	5
of virus transmission	5
the proportion of	5
we hope that	5
was reported in	5
pairwise aa identity	5
most frequent in	5
of host cell	5
submitted to the	5
of the polymerase	5
south korea and	5
for this study	5
from the same	5
third of the	5
host on the	5
majority of the	5
most of these	5
for vaccine development	5
in comparison to	5
of bovine kobuvirus	5
the spike glycoprotein	5
in the future	5
course of the	5
strains from china	5
sequence identities of	5
of the receptor	5
with acute diarrhea	5
been isolated from	5
we predicted the	5
f protein is	5
supports bat coronaviruses	5
strains detected in	5
which is a	5
genetic and antigenic	5
of diagnostics and	5
a final concentration	5
the canine nov	5
quality of the	5
strains from the	5
may also be	5
new coronavirus of	5
amino acid level	5
in dogs in	5
betacoronavirus and avian	5
of the viruses	5
a measure of	5
ck ch lsc	5
this study and	5
viseu prt and	5
pneumonia outbreak associated	5
for min and	5
nsp proteins from	5
ifng a t	5
the host population	5
and s rrna	5
of infectious diseases	5
on the phylogenetic	5
aragones et al	5
for peptide vaccine	5
the innate immune	5
have been observed	5
most commonly used	5
final concentration of	5
to make the	5
analyses of the	5
time of the	5
early epidemic scovs	5
of cases of	5
in the a	5
virus codon usage	5
a child with	5
analyses were performed	5
mouse hepatitis virus	5
with signs of	5
primers used for	5
fekov strains identified	5
infected with sars	5
number of patients	5
graham and baric	5
genotypes with the	5
the s genes	5
a retrospective study	5
this virus in	5
that the sars	5
antiviral therapeutic drugs	5
the feline nov	5
and the potential	5
was collected from	5
coding sequences for	5
and severe acute	5
was compared with	5
can also be	5
analysis of sars	5
on the same	5
the plots for	5
start of the	5
be due to	5
the family coronaviridae	5
in pigs and	5
in s and	5
our understanding of	5
argentina and brazil	5
paraskevis et al	5
a and orf	5
the results showed	5
the fcv orf	5
at the national	5
of nucleotide substitutions	5
been used to	5
the basis of	5
the identification of	5
and of the	5
variation in the	5
in all the	5
virus and its	5
coronaviruses in poultry	5
bat coronaviruses as	5
pravica et al	5
amino acid position	5
viruses isolated from	5
in the third	5
discovery of seven	5
hepatitis b virus	5
total rna was	5
of rab were	5
codon usage variation	5
extent of codon	5
in the atlantic	5
a maximum likelihood	5
higher than those	5
a peptide vaccine	5
of the nov	5
development of cardiomyopathy	5
implications for the	5
the similarity degree	5
strains circulating in	5
be useful for	5
of viral proteins	5
across the entire	5
pairs of primers	5
like infectious bronchitis	5
study aimed to	5
were identified to	5
the viruses from	5
pneumonia in wuhan	5
deltacoronavirus supports bat	5
epidemiology of human	5
and p genotypes	5
the treatment of	5
were classified as	5
borrelia burgdorferi sensu	5
genome sequence analysis	5
recombination detection program	5
had a higher	5
avian coronaviruses as	5
role in shaping	5
the roles of	5
a period of	5
resulting in the	5
each of the	5
of the paramyxoviridae	5
nl nsp proteins	5
not detected in	5
and sylvatic genotypes	5
virus ns protein	5
republic of china	5
a large fraction	5
of occurrence of	5
uniprot protein information	5
antagonize host innate	5
a highly contagious	5
presence of antibodies	5
study showed that	5
verhagen et al	5
sequences of sars	5
to analyze the	5
features of the	5
hosts of emerging	5
were purified using	5
the p genotype	5
depends on the	5
generalized skyline plot	5
from uniprot protein	5
according to their	5
the cause of	5
a group of	5
form of the	5
substitutions per site	5
from different countries	5
genetic variability of	5
of feline calicivirus	5
of novs in	5
h n virus	5
evaluation of a	5
in the transmission	5
a pneumonia outbreak	5
be further investigated	5
strain isolated from	5
nt in length	5
evolutionary dynamics of	5
are present in	5
the discovery of	5
values of all	5
the start of	5
and antigenic characteristics	5
in patients with	5
bats to humans	5
our selected peptides	5
helvum in zambia	5
of molecular evolution	5
the murine coronavirus	5
the context of	5
fruit bats in	5
seven novel mammalian	5
hoffmann et al	5
of the full	5
for the vp	5
at the time	5
vennema et al	5
were similar to	5
and the highest	5
showed that all	5
almeida et al	5
the genetic characteristics	5
of a porcine	5
and betacoronavirus and	5
presence of nov	5
of the fcv	5
protein is the	5
the genome sequences	5
structure and function	5
the exception of	5
evolution of ev	5
binding domain of	5
lack of a	5
santiago et al	5
small number of	5
been described in	5
sequences obtained in	5
highest immunogenicity score	5
full s coding	5
t mrca of	5
molecular analysis of	5
been identified as	5
new england biolabs	5
belouzard et al	5
evidence of recombination	5
the borrelia spp	5
based on their	5
veterinary research institute	5
position of the	5
prevalence of iav	5
was done using	5
of fekov in	5
near the breakpoint	5
recombination within the	5
of population size	5
of seven novel	5
have shown that	5
for receptor binding	5
first time in	5
s rrna sequences	5
and vaccine design	5
epitopes from the	5
well as the	5
that the reemerging	5
the ibv genome	5
were not detected	5
studies have been	5
innate immune responses	5
no conflicts of	5
a wide range	5
involved in the	5
the republic of	5
capsid protein vp	5
total number of	5
unique early polish	5
characterization of feline	5
these results indicate	5
mhc class i	5
development of diagnostics	5
march to april	5
the genus deltacoronavirus	5
numbers are shown	5
of the murine	5
primers were designed	5
associated with severe	5
of human enterovirus	5
protein information for	5
needs to be	5
to determine whether	5
declare that they	5
viruses in wild	5
human coronavirus oc	5
infected with hiv	5
to possess the	5
an independent branch	5
to develop a	5
commonly used vaccine	5
herpes simplex virus	5
the beginning of	5
are likely to	5
and fd ita	5
the first and	5
pinto et al	5
it is possible	5
and codon usage	5
of gammacoronavirus and	5
the virus and	5
and nucleotide contents	5
by a single	5
and other birds	5
an in silico	5
of rna virus	5
order to find	5
were constructed using	5
close relationship with	5
comparative genome analysis	5
role of bats	5
comparison of the	5
transmissible gastroenteritis virus	5
of origin of	5
of open reading	5
the full s	5
of the presence	5
and healthy controls	5
and the codon	5
geographic and social	5
genetic susceptibility to	5
ribosomal s subunit	5
trento et al	5
resulted from a	5
characterization of infectious	5
of alphacoronavirus and	5
antigenic characteristics of	5
in the evolution	5
to be more	5
viral replication and	5
been associated with	5
cats with diarrhea	5
same amino acid	5
the cells were	5
the host immune	5
by the virus	5
in virus genomes	5
to find the	5
the ifng a	5
cov and sars	5
reported in this	5
that they have	5
discovery of a	5
the open reading	5
portion of the	5
immune sera against	5
and the results	5
is an important	5
evolutionary history of	5
only a few	5
source of alphacoronavirus	5
report of the	5
large fraction of	5
isolated in the	5
under the accession	5
the human population	5
host immune response	5
of these strains	5
used in the	5
a new model	5
the b strain	5
a new genotype	5
in comparison with	5
as observed in	5
respiratory syncytial viruses	5
data suggest that	5
cats in northeast	5
the pathogenicity of	5
cases of infection	5
remains to be	5
grouped into four	5
pcr assay for	5
the same amino	5
source of gammacoronavirus	5
and it is	5
natural reservoirs of	5
recurrent mutations in	5
duplication in the	5
suggests that the	5
tree was generated	5
of the ck	5
addition to the	5
single open reading	5
the most important	5
they have no	5
wit et al	5
also observed in	5
analysis of human	5
nl and sars	5
as a consequence	5
the enc values	5
indicating that the	5
in hong kong	5
performed with the	5
the relationship of	5
coronavirus avian infectious	5
was isolated in	5
respiratory disease of	5
bats are the	5
study reported that	5
viruses isolated in	5
are needed to	5
bhattacharyya et al	5
the h vaccine	5
and is a	5
were in the	5
to the previous	5
fraction of the	5
were more closely	5
for this purpose	5
such as those	5
nj and pars	5
were stored at	5
for the sars	5
s genes of	5
from the s	5
in e protein	5
was performed to	5
were identified using	5
coronavirus of probable	5
innate immune system	5
referred to the	5
diversity and evolution	5
and molecular epidemiology	5
may represent a	5
available in genbank	5
of newcastle disease	5
genetic variants in	5
were associated with	5
is caused by	5
the highest immunogenicity	5
cause of severe	5
nsp genes of	5
viruses in the	5
from the other	5
play roles in	5
a correlation between	5
with the human	5
was analyzed with	5
multiple reassortment events	5
pathogenesis of coronaviruses	5
in cambodia and	5
the ifng t	5
the generalized skyline	5
bronchitis virus strain	5
length vp amino	4
detected across the	4
the spike gene	4
in new zealand	4
in the innate	4
and aligned using	4
were identified with	4
aim of this	4
gene of rab	4
effective population size	4
ramey et al	4
population dynamics of	4
relies on the	4
under the following	4
franzo et al	4
moratorio et al	4
first molecular evidence	4
whitney u test	4
in vero ccl	4
ita and fd	4
corresponding amino acid	4
were considered to	4
frame shift protein	4
similarity of the	4
a target for	4
at c for	4
xiao et al	4
in previous reports	4
the prefusion conformation	4
similarity degree between	4
only a single	4
high mutation rate	4
closest to the	4
to be of	4
novel coronavirus pneumonia	4
of human adenovirus	4
becker et al	4
from march to	4
resulted in a	4
to the h	4
from the coronavirus	4
to study the	4
circulation of novs	4
to trypanosoma cruzi	4
and the effects	4
to chagas disease	4
the cai values	4
type i interferon	4
full genome sequence	4
h and m	4
the hexon gene	4
south east asia	4
the most commonly	4
method for the	4
aga in the	4
guindon et al	4
in dogs and	4
miseq reagent kit	4
interaction with the	4
complete vp sequences	4
in children with	4
epidemiological and clinical	4
for viral entry	4
solomon et al	4
plays a major	4
was funded by	4
female balb c	4
formed a separate	4
the adaptation of	4
strains based on	4
has recently been	4
i binding epitopes	4
according to previous	4
the serotype of	4
new model for	4
flab fragments belonging	4
canine norovirus in	4
has been suggested	4
orfs in the	4
ibv strains showed	4
coronavirus spike glycoprotein	4
substitutions site year	4
local alignment search	4
type i ifn	4
not significantly different	4
influenza virus in	4
cruzi infection in	4
old female balb	4
whole genome of	4
vp and nsp	4
be the result	4
model for the	4
two or more	4
one step rt	4
the prevention and	4
the city of	4
vero e cells	4
protein sequences were	4
for the complete	4
provinces in china	4
influenza a h	4
that strains ck	4
bradley and altizer	4
the antigenic relatedness	4
that of host	4
fragmentation index and	4
and genomic characteristics	4
the vp region	4
agg in the	4
rab was closely	4
epidemiology and evolution	4
of the swine	4
at least three	4
identity to the	4
is a highly	4
is essential to	4
ev and that	4
amplification and sequencing	4
the reference sequence	4
titrated with purified	4
causative agent of	4
web version of	4
s protein was	4
azevedo et al	4
of an epitope	4
the group i	4
s gene sequence	4
of vp and	4
the sample was	4
of emerging infectious	4
nucleotide duplication in	4
simple method for	4
was synthesized using	4
phylogenetic analysis and	4
the a allele	4
borrelia species obtained	4
this was not	4
flab and s	4
are shown after	4
circulating in china	4
on the tree	4
origin of sars	4
it is a	4
the numbers of	4
genomes with the	4
was shown in	4
contributed to the	4
was inferred using	4
of the immune	4
are responsible for	4
by the host	4
was located in	4
of the new	4
and to the	4
the most prevalent	4
epitopes of jev	4
around the globe	4
other birds coronavirus	4
third site of	4
review of the	4
the function of	4
of the gi	4
some studies have	4
host immune and	4
of h n	4
evolution of human	4
rapidly evolving viruses	4
the nsp protein	4
the gb strain	4
of dna sequences	4
to the human	4
western blot analysis	4
using the neighbor	4
bats were collected	4
indicated by bold	4
been reported that	4
of s glycoprotein	4
was recorded with	4
relative genetic diversity	4
supplementary data associated	4
host gene expression	4
effect of the	4
determinant of the	4
was conducted using	4
shaping codon usage	4
virus genotypes in	4
found to have	4
out of these	4
in horseshoe bats	4
of viral replication	4
sequence in the	4
west nile virus	4
variations in the	4
half of the	4
bats in the	4
from recombination events	4
is yet to	4
is that the	4
have been shown	4
topology of the	4
we have found	4
the first on	4
with sars coronavirus	4
phylogenetic analysis revealed	4
full genomic analysis	4
the aim of	4
in the natural	4
purified and cloned	4
tumor necrosis factor	4
in this analysis	4
data were eliminated	4
virus strains from	4
ns of jev	4
joining method of	4
used to characterize	4
the department of	4
in the hvrs	4
based on these	4
and those deposited	4
known about the	4
bats as a	4
showed that of	4
van dijk et	4
that all the	4
this is in	4
sequence alignment of	4
the sylvatic genotype	4
to the gi	4
maximum parsimony methods	4
were present in	4
cats and dogs	4
was found that	4
in the lasergene	4
the form of	4
of bat viruses	4
the regulation of	4
a g gene	4
from a dog	4
effective number of	4
ebola virus vp	4
guo et al	4
tree was inferred	4
in bats from	4
is described by	4
bronchitis viruses isolated	4
the relative genetic	4
alignment search tool	4
were successfully obtained	4
a monophyletic clade	4
implications for virus	4
in the utr	4
leading to the	4
interaction between mutation	4
limited understanding of	4
in the prefusion	4
gu et al	4
summa et al	4
west bengal and	4
clinical signs of	4
of the evolution	4
of s protein	4
highlighted in red	4
nucleotide sequences located	4
gc s values	4
the hvr encoding	4
mutation in sars	4
version of this	4
this strain was	4
baek et al	4
related to those	4
human adenovirus type	4
were most closely	4
a descriptive study	4
fecal samples of	4
vp is the	4
the pcr conditions	4
in genbank from	4
evidence for recombination	4
of the species	4
similar to sars	4
cell epitopes in	4
a survey of	4
this figure legend	4
a consensus sequence	4
of the coalescent	4
it was reported	4
genomic characteristics of	4
point mutations as	4
of this article	4
that for the	4
the first molecular	4
the us strain	4
are shown at	4
reed and muench	4
ibv strains are	4
a reference for	4
from the present	4
of the coronaviridae	4
sodhi et al	4
epidemiology of infectious	4
the epidemic strain	4
choi et al	4
and genetic diversity	4
in infected cells	4
for ser were	4
position in the	4
were performed in	4
which in turn	4
samples were positive	4
divided into two	4
like to acknowledge	4
smith et al	4
characteristics of cases	4
strains available in	4
between mutation pressure	4
angiotensin converting enzyme	4
first isolation of	4
isolated from an	4
in different host	4
identical to the	4
sequences located at	4
epithelial cells of	4
of this polymorphism	4
and clinical characteristics	4
of ev virus	4
biological sequence alignment	4
protein of avian	4
zhong et al	4
was in the	4
genotypes of infectious	4
the web version	4
represent a novel	4
the antigenicity of	4
unique aa mutations	4
and the development	4
the seven hvrs	4
positive for crcov	4
the genetic variation	4
amino acid differences	4
high frequency of	4
between bstvs and	4
population genetic models	4
the help of	4
the feline strain	4
necessary to continue	4
in the context	4
strains and the	4
be noted that	4
and have been	4
which is consistent	4
and other animal	4
identification of the	4
assessment of the	4
respiratory distress syndrome	4
emerged from the	4
infected with mers	4
very similar to	4
with the following	4
the impact of	4
clc genomics workbench	4
and approved the	4
protein synthesis by	4
probability of the	4
were retrieved from	4
of group a	4
in association with	4
the variation in	4
akaike information criterion	4
rna virus and	4
transmission of the	4
sequences were obtained	4
using the complete	4
the type of	4
to the chinese	4
the human scovs	4
a detailed comparative	4
science and technology	4
ch ldl and	4
the us and	4
the sars epidemic	4
was confirmed using	4
norovirus in dogs	4
viruses have been	4
the same way	4
the viral rna	4
than those in	4
strains from different	4
virus from a	4
of the on	4
of s rrna	4
in the past	4
from cats with	4
application to the	4
virus isolates from	4
from the presence	4
in the nidovirales	4
andersen et al	4
serological and molecular	4
sequences were used	4
for statistical computing	4
in a colombian	4
the consensus sequence	4
were performed with	4
rscu value of	4
to the epidemic	4
the phylogeography of	4
of the cbuv	4
values are shown	4
in china in	4
in the full	4
with the help	4
cell epitopes using	4
parrish et al	4
seems to be	4
was detected from	4
cao et al	4
of an epidemic	4
support from replications	4
a fast and	4
total net charges	4
the genomic diversity	4
chemokine genes in	4
at each branch	4
sequences of polish	4
as a vaccine	4
or in mixed	4
gene of sccd	4
in five proteins	4
early polish variants	4
of darwinian selection	4
from the sequence	4
and agg in	4
receptor binding domain	4
aku of s	4
han et al	4
cases of novel	4
the genomic and	4
region of india	4
occurrence of recombination	4
of the borrelia	4
reader is referred	4
a colombian population	4
other rna viruses	4
to infer the	4
the sequence alignment	4
genetically related to	4
s subunit was	4
focused on the	4
mutation pressure and	4
g in the	4
at the c	4
is the similarity	4
receptor for the	4
dynamics of human	4
n influenza a	4
gene showed that	4
genomic diversity of	4
asanaka et al	4
each branch point	4
are presented in	4
moore et al	4
associated with human	4
complete genomic sequence	4
in the summer	4
o f key	4
the ba genotype	4
of which are	4
optimal codons with	4
canine nov strains	4
vp gene were	4
in close proximity	4
sequence alignment software	4
a key factor	4
branch of the	4
the following accession	4
rotavirus g p	4
shown at each	4
shown after isolate	4
bias in the	4
of ev were	4
immunogenic vaccine peptide	4
years in china	4
epitope or a	4
to possess high	4
virus prevalence and	4
the expression of	4
to be determined	4
purified using the	4
acid substitutions were	4
the virus population	4
protein of the	4
gene analysis of	4
are natural reservoirs	4
the third site	4
the structured coalescent	4
the same serotype	4
the bactrian camel	4
for interpretation of	4
of homolog proteins	4
clustered in the	4
for the non	4
the type i	4
within the genogroup	4
showed that strains	4
the remaining non	4
most of them	4
from each other	4
to the fact	4
nt in the	4
have been discovered	4
was constructed with	4
was also found	4
n protein is	4
when compared with	4
number of mutations	4
that the nsp	4
is expected to	4
from asymptomatic animals	4
have been assessed	4
a nested pcr	4
yu et al	4
the nucleotide sequence	4
in the viral	4
collected from a	4
novel coronavirus from	4
friendly biological sequence	4
with chagas disease	4
virus isolated in	4
in presence of	4
samples were detected	4
virus to the	4
virus detected in	4
the supernatant was	4
and ecology of	4
of their hosts	4
lead to the	4
values were calculated	4
g p genotype	4
of antibodies against	4
key determinant of	4
qiaquick gel extraction	4
detection and genetic	4
of new variants	4
over the past	4
with purified core	4
option complete deletion	4
frequency of the	4
primer sequences are	4
the need for	4
iav and cov	4
and induction of	4
the estimation of	4
virus in wild	4
chinese fekov strains	4
sz and sz	4
the recombination detection	4
orf of the	4
and all the	4
viruses and their	4
cases and deaths	4
was that of	4
and results in	4
play an important	4
analysis on the	4
genbank from different	4
in genetic diversity	4
ch lhlj and	4
previous study reported	4
the host receptor	4
followed by cycles	4
coronavirus and canine	4
the highest hydrophilicity	4
genetic sequence data	4