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Journal of Virology, September 2000, p. 7980-7988, Vol. 74, No. 17
0022-538X/00/$04.00+0
The Genome of a Very Virulent Marek's
Disease Virus
E. R.
Tulman,
C. L.
Afonso,
Z.
Lu,
L.
Zsak,
D. L.
Rock, and
G. F.
Kutish*
Plum Island Animal Disease Center,
Agricultural Research Service, U.S. Department of Agriculture,
Greenport, New York 11944
Received 20 April 2000/Accepted 24 May 2000
 |
ABSTRACT |
Here we present the first complete genomic sequence, with analysis,
of a very virulent strain of Marek's disease virus serotype 1 (MDV1),
Md5. The genome is 177,874 bp and is predicted to encode 103 proteins.
MDV1 is colinear with the prototypic alphaherpesvirus herpes simplex
virus type 1 (HSV-1) within the unique long (UL) region, and it is most
similar at the amino acid level to MDV2, herpesvirus of turkeys (HVT),
and nonavian herpesviruses equine herpesviruses 1 and 4. MDV1 encodes
55 HSV-1 UL homologues together with 6 additional UL proteins that are
absent in nonavian herpesviruses. The unique short (US) region is
colinear with and has greater than 99% nucleotide identity to that of
MDV1 strain GA; however, an extra nucleotide sequence at the Md5
US/short terminal repeat boundary results in a shorter US region and
the presence of a second gene (encoding MDV097) similar to the SORF2
gene. MD5, like HVT, encodes an ICP4 homologue that contains a
900-amino-acid amino-terminal extension not found in other
herpesviruses. Putative virulence and host range gene products
include the oncoprotein MEQ, oncogenicity-associated phosphoproteins
pp38 and pp24, a lipase homologue, a CxC chemokine, and unique proteins
of unknown function MDV087 and MDV097 (SORF2 homologues) and MDV093
(SORF4). Consistent with its virulent phenotype, Md5 contains only two copies of the 132-bp repeat which has previously been associated with
viral attenuation and loss of oncogenicity.
| |
INTRODUCTION |
Marek's disease (MD) is a
lymphoproliferative disease of chickens caused by the highly infectious
cell-associated alphaherpesvirus MD virus serotype 1 (MDV1)
(18). Yearly economic losses from MD total $1 billion
worldwide (18). MDV1 infection results in a rapid onset of
malignant T-cell lymphomas within several weeks of infection. Tumor
infiltration results in a neural form of disease, which causes
progressive paralysis, or a visceral form of disease, which is usually
very acute and accompanied by high mortality. Productive virus
replication in the skin and feather follicle epithelia with subsequent
virus shedding is responsible for disease transmission (18).
MD is controlled by vaccination and good management practices
(18). Naturally occurring nonpathogenic strains of MDV1,
MDV2, and herpesvirus of turkey (HVT or MDV3) have been used
individually or together in bivalent vaccines (18, 40).
Recent increases in MD-related mortality and condemnations among
vaccinated poultry have occurred in the United States. These increases
in disease have occurred approximately 6 years after the introduction
of new vaccines (99). In the late 1970s, following the
introduction of HVT vaccines, and since 1992, after the introduction of
bivalent MDV2-HVT-based vaccines, new MDV1 strains of greater virulence (very virulent [vv] and very virulent plus [vv+] MDV1)
were isolated. These viruses are characterized by higher cytolytic
activity, unusual tissue tropism, increased atrophy of lymphoid organs,
immunosuppression, enhanced capacity to transform T cells, and earlier
host death (7, 17, 99). It has been suggested that emergence
of vv and vv+ MDV1 strains may be due to strong selective
pressure generated by extensive vaccination and enhanced genetic
resistance of commercial flocks (99).
To date, MDV1 genome characterization has involved partial sequencing
of several different virus strains, accounting for approximately 40%
of the complete genome (reviewed in reference 8).
However, the genetic basis and molecular mechanisms underlying viral
virulence and oncogenicity remain poorly understood. Genes encoding
proteins involved in T-cell transformation (MEQ) and others with
potential involvement in tumorigenicity, viral virulence, and host
range (pp24, pp38, interleukin 8 [IL-8], SORF2) have been described (14, 24, 43, 57, 65, 66, 79, 89, 90, 102, 109). Additionally, virus attenuation has been associated with amplification of a 132-bp repeat within the long repeats (10-12, 34, 61, 78,
90). To improve understanding of MDV virulence and the mechanisms
associated with enhanced viral virulence, more-complete information
about the MDV genome and its gene complement is needed. Here we present
the first complete genome sequence, with analysis, of a vv MDV1
isolate, Md5 (100).
| |
MATERIALS AND METHODS |
DNA isolation, cloning, and sequencing.
The Md5 strain of
MDV was obtained from the American Type Culture Collection (Manassas,
Va.) and passaged three times in primary chicken embryo fibroblast cell
cultures. Viral DNA was extracted from the cytoplasm of infected cells
as previously described (98). Random DNA fragments were
obtained by incomplete enzymatic digestion with TaqI and
AciI endonucleases (New England Biolabs, Beverly, Mass.).
DNA fragments of 1.5 to 2.5 kbp were isolated after separation on
agarose gels, cloned into the dephosphorylated AccI site of pUC19 plasmids, and grown in Escherichia coli DH10B cells
(Gibco BRL, Gaithersburg, Md.). Plasmids were purified by alkaline
lysis according to the manufacturer's instruction (Eppendorf 5 Prime, Boulder, Colo.). DNA templates were sequenced from both ends with M13
forward and reverse primers using dideoxy chain terminator sequencing
chemistries (82) and the Applied Biosystem PRISM 377 automated DNA sequencer (PE Biosystems, Foster City, Calif.). ABI
sequencing analysis software (version 3.3) was used for lane tracking
and trace extraction. Bases were called from chromatogram traces with
Phred (30), which also produced a quality file containing a
predicted probability of error at each base position.
DNA sequence analysis.
DNA sequences were assembled with
Phrap (29) using the quality files and default settings to
produce a consensus sequence, which was manually edited with Consed
(37). An identical sequence was assembled using the TIGR
assembler with quality files and clone length constraints
(95). Gap closure was achieved by primer walking of
gap-spanning clones and sequencing of PCR products. The final DNA
consensus sequence represented on average sixfold redundancy at each
base position. The predicted restriction map for Md5 matched published
data for the MDV1 GA strain (15). For descriptive purposes,
we have presented Md5 in a linearized fashion as described by Dolan et
al. (28). Genome DNA composition, structure, repeats, and
restriction enzyme patterns were analyzed as previously described
(2). Open reading frames (ORFs) encoding proteins of greater
than or equal to 60 amino acids with a methionine start codon (92,
93) were evaluated for coding potential using the Hexamer
(ftp.sanger.ac.uk/pub/rd) and Glimmer (81) computer programs. Other criteria included similarity to other herpesvirus or
cellular proteins, published evidence for MDV proteins, and compact
gene arrangement with little gene overlap (25, 96). Homology
searches were conducted using Blast (3), PsiBlast (4), FASTA (70), and HMMER (16)
programs with the following databases: PROSITE, Pfam, Prodom, Sbase,
Blocks, Domo, and GenBank (16). GCG (26), MEMSAT
(50), and SAPS (13) programs were used for gene
analysis. Published mRNA and cDNA data were compared to the Md5 genomic
sequence using the Est_genome (ftp.sanger.ac.uk/pub/EMBOSS) and Sim4
(33) alignment programs.
Nucleotide sequence accession number.
The MDV1 Md5 genome
sequence has been deposited in GenBank under accession no. AF243438.
| |
RESULTS AND DISCUSSION |
Genome organization.
The Md5 genome is 177,874 bp long and
contains a 44% G+C base composition. Md5 is organized in the same
overall manner as other alphaherpesviruses (75). Long and
short unique regions (UL and US regions, respectively) are 113,563 and
10,847 bp in length, respectively. Each unique region is bounded by
identical inverted repeats. The terminal and internal UL repeats (TRL
and IRL, respectively) are 13,065 bp, and the internal and terminal US
repeats (IRS and TRS, respectively) are 12,264 bp. As with other
herpesviruses, the G+C content in the repeat regions is higher than
that in the unique regions (49 to 50% in repeats versus 41 to 42% in
unique regions) (25, 36, 96). Md5 does not contain the
retroviral long terminal repeat sequences previously reported at the
US/short repeat boundary of cell culture-passaged MDV1 strains
(44, 47, 48).
Alphaherpesvirus 
-type sequences are located at the genomic termini
and at the IRL/IRS junction of Md5. They consist of 7 tandem copies of
a 60-bp repeat associated with the long direct repeat, a 43-bp unique
spacer sequence, and 64 tandem copies of a 6-bp repeat associated with
the short direct repeat (28, 52, 53, 96). As previously
reported, the 6-bp repeat is identical to repetitive sequences in the
direct repeats of human herpesvirus 6 and in eukaryotic telomeres
(53).
Gene characterization.
Md5 contains 338 ORFs encoding proteins
of 60 or more amino acids of which 103 are likely to be functional
genes (Table 1). Seventy-three genes are
present as single copies and initiate within
unique regions. Thirty genes initiate and are partially or completely located within repeat regions, including two genes within
-sequence regions. MDV004, MDV007, MDV075, MDV077, MDV086, and
MDV098 ORFs were annotated here because previous reports indicated that
these ORFs were protein coding (41, 67, 72). Most Md5 genes
are virtually identical (99% nucleotide and amino acid identity) to
published genes from other MDV1 strains and less similar to those from
MDV2 (40 to 86% amino acid identity) and HVT (38 to 81% amino acid
identity). Among nonavian herpesviruses, EHV1 and EHV4 are generally
the most similar to Md5 (25 to 61% amino acid identity).
UL region.
The UL region, extending from nucleotide positions
14029 to 127591, contains 64 genes of which 38 have not been previously described (Fig. 1, Table 1). MDV013 to
MDV070 genes, which represent 57% of the Md5 genome, are colinear with
UL1 to UL55 genes of herpes simplex virus type 1 (HSV-1). Proteins
encoded by these Md5 genes are 22 to 61% identical to HSV-1 homologues
and 42 to 86% identical to MDV2 homologues. Capsid proteins MDV030,
MDV031, and MDV048, DNA replication proteins MDV017, MDV021, MDV042,
MDV043, MDV055, and MDV066, nuclear proteins MDV015 and MDV044, and
glycoproteins MDV022, MDV040, and MDV057 encoded in the UL are highly
conserved with homologues in MDV2 (66 to 86% amino acid identity).
Tegument proteins (MDV023, MDV033, MDV049, MDV059, MDV060, and MDV062) and membrane proteins MDV032 and MDV056 are less conserved (42 to 65%
amino acid identity). Viral enzymes MDV025, MDV052, MDV055, and MDV063
contain notable insertions and deletions compared to MDV2 homologues.
MDV009, MDV010, MDV011, MDV012, MDV069, and MDV072 genes, located at
the ends of the UL region, are absent in nonavian herpesviruses such as
HSV and equine herpesvirus (EHV), suggesting a possible role for these
genes in avian host range.
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FIG. 1.
Linear map of the Md5 genome. Genes (colored arrows) are
numbered from left to right based on position of methionine initiation
codons. Genes and RNA transcript regions (black-and-white arrows) are
transcribed in the directions indicated. Genomic regions are defined in
the color key. Yellow boxes, regions of 132-bp repeats. Nucleotide
positions are indicated above the map.
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|
The MDV010 gene encodes a 684-amino-acid protein that is similar to
other viral proteins and to known eukaryotic lipases (Fig.
2). The gene for the MDV010 homologue in
MDV1 strain GA (MDV1
GA) has previously been shown to be spliced
(
9). The predicted
protein contains the serine active site
within the lipase signature
motif (Prosite PS00120) (Fig.
2) and
conserved cysteines involved
in disulfide bond formation (amino acid
positions 416 and 438).
The region between amino acids 216 and 374 is
similar to those
in eukaryotic lipases such as phospholipase A1 and
triacylglycerol
lipase. Similarity to predicted proteins from MDV2 and
fowl adenovirus
extends beyond this region, suggesting the presence of
virus-specific
domains. The presence of a signal peptide in the
amino-terminal
domain and a transmembrane domain at amino acid
positions 540
to 553 suggest that MDV010 may be membrane localized.
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FIG. 2.
Multiple amino acid sequence alignment of MDV010 with
lipases. Asterisks, conserved sites at lipase Prosite signature
(PS00120); boldface, serine active sites; shaded residues, amino acid
identity to MDV010. Amino acid positions are indicated on the right.
Avianadeno, avian adenovirus 8, accession no. AF021254; squirrel,
Spermophilus tridecemlineatus, accession no. AF027293; pig,
Sus scrofa domestica, accession no. P00591; wasp,
Vespula vulgaris, accession no. L43561; MDV2, accession no.
AB024414; MDV1, Md5 isolate, MDV010.
|
|
Type A1 phospholipases have been identified in many mammalian tissues
(platelets, liver, and heart) as membrane-bound or cytosolic
enzymes
which catalyze transacylation reactions (
39,
64,
83).
Phospholipase A1 activity on phosphatidic acid substrates may
modify
intracellular second-messenger pathways (
39). Modification
of host cell second-messenger pathways has been observed with
other
virus infections (
1,
27,
87). Human herpesvirus 8
(Kaposi's
sarcoma-associated herpesvirus) encodes a G protein-coupled
receptor
which activates phospholipase C and which stimulates
cell proliferation
and transformation (
35). Both cytomegalovirus
and adenovirus
affect arachidonic acid metabolism through pathways
involving
phospholipase A2 (
1,
27). Arachidonic acid is a
precursor to
prostaglandins, leukotrienes, and lipoxins, molecules
which modify
inflammatory responses. Altered lipid metabolism
has been observed both
in vivo and in cell cultures during MDV
infection (
32,
38).
MDV010 may perform host range functions
involving alteration of host
lipid metabolism and/or modification
of second-messenger signaling
pathways.
US region.
The US region, extending from positions 153799 to
164645 (10,847 bp), contains nine genes (encoding MDV088 to MDV097),
which include homologues of the HSV-1 US1, US2, US3, US6, US7, US8, and
US10 genes. The MDV1 GA US region has previously been completely sequenced (11,160 bp), and the MDV1 RB1B US region has been partially sequenced (14, 76). Md5 ORFs are colinear with and virtually identical (>99% nucleotide identity) to ORFs from these two MDV1 strains. Md5 contains sequences at the US/TRS boundary (nucleotide positions 164033 to 164518 and 164636 to 165464) that are absent in
MDV1 GA. Due to the expansion of the TRS, the Md5 US region is 313 nucleotides shorter than the US region of MDV1 GA. As has been
previously reported, the arrangement of genes in the MDV1 US region
differs from those of other alphaherpesviruses. The MDV089 gene (US10
gene homologue) is inverted and translocated compared to the US10 gene
in HSV-1, and no homologues of HSV-1 US genes are located in the short
repeat regions as they are in pseudorabies virus (PRV), EHV, and
varicella-zoster virus (VZV) (14, 25, 62, 76, 96, 108).
The arrangement of genes in the Md5 US region is similar to that in the
US regions of MDV2 and HVT (
46,
106). Proteins
encoded in
the Md5 US region are 47 to 72% and 40 to 66% identical
to their
homologues in MDV2 and HVT, respectively. MDV090, previously
described
as SORF3, is unique to the avian herpesviruses MDV1,
MDV2, and HVT
(
106). MDV093 (SORF4) is unique to MDV1 (
14,
46,
106). Absence of the MDV093 gene in nonpathogenic MDV2
and HVT
suggests a possible role in viral
virulence.
Long repeats.
The long repeat regions are 13,065 bp located at
nucleotide positions 964 to 14028 and 127592 to 140656. These repeat
regions contain 16 genes, all of which are unique to MDV1. Proteins
from three of these genes associated with cellular transformation
include the Marek's EcoRI Q fragment protein (MEQ), which
is present in two copies (MDV005 and MDV076), pp38 (MDV073), and pp24
(MDV008) (24, 79, 90, 102, 109).
MDV005 and MDV076 genes encode MEQ, a 339-amino-acid basic region
leucine zipper protein (
49). MEQ is a transcriptional
transactivator and potential oncoprotein detected in MDV-induced
tumors
and cell lines and has been shown to induce and maintain
transformed
cell phenotypes, protect transformed cells from apoptosis,
and
colocalize with cyclin-dependent kinase 2 in a cell cycle-dependent
manner (
49,
58,
59,
73,
102). Compared to MEQ from MDV1
GA,
MDV005 and MDV076 contain amino acid substitutions at positions
Ala 217 within the second full proline-rich repeat, Val 283, and
Thr 320. The
MDV004 and MDV077 genes are antisense to the MEQ
gene and homologues of
an ORF previously shown to encode a 23-kDa
nuclear protein expressed in
MDV-transformed lymphoblastoid cells
(
72).
The MDV008 and MDV073 genes encode oncogenicity-related
phosphoproteins pp24 and pp38, respectively (
21). pp24
and pp38
are among the first MDV proteins expressed in
MDV-induced tumors
and are part of a phosphorylated protein complex
present in MDV-induced
lymphoblastoid cell lines (
43,
65,
66,
89). These genes
span the long repeat/UL boundary (
60,
109). The two proteins
share 65 amino acids at their amino
termini, which are encoded
in the long repeats, while their carboxyl
termini are encoded
at either end of the UL region (
60,
109). Interestingly, these
two proteins have carboxyl-terminal
amino acid similarity that
has not been previously described. Conserved
amino acids include
a DLLVEAE motif (amino acid positions 85 to 91 in
MDV008 and 163
to 169 in MDV073) and a region of 30% amino acid
identity (amino
acid positions 93 to 155 of MDV008 and 213 to 275 of
MDV073).
MDV2 pp24 and pp38 homologues and an HVT pp38 homologue do not
contain the amino-terminal domains present in MDV1 proteins (
68,
91). Given that MDV2 and HVT are nononcogenic, the novel
amino-terminal
regions present in MDV1 homologues may play some role in
viral
virulence and/or
oncogenicity.
The MDV003 and MDV078 genes are spliced genes with homology to genes
encoding mammalian CxC chemokines (Table
1). This gene
was previously
described as encoding an IL-8 homologue; however,
IL-8 activity was not
demonstrated (
57). The MDV003 and MDV078
genes each comprise
three exons, and the proteins share 41% amino
acid identity with
murine macrophage inhibitory protein 2 (MIP-2)
and contain the four
cysteine residues necessary for disulfide
bonding. The amino-terminal
region, which defines receptor-binding
specificity, is less similar to
those of MIP-2 and other CxC chemokines
than is the carboxyl-terminal
region (
23). Chemokines mediate
immune cell activation and
migration during inflammation (
6).
Chemokine homologues
encoded by other herpesviruses have been
shown to function as either
agonists or antagonists (
54). An
MDV-encoded chemokine may
function in immune evasion by affecting
host inflammatory responses.
Chemokines have also been associated
with vasculopathologies such as
atherosclerosis and transplant
vascular sclerosis (
97).
Atherosclerotic lesions including proliferative
changes in arteries
have been observed in MDV-infected chickens
(
31).
Conceivably, the MDV-encoded chemokine may be involved
in
MDV-associated
atherosclerosis.
A family of 1.8-kb RNAs mapping to the long repeat region has been
associated with oncogenicity (
11,
12,
51,
78) (Fig.
1).
Transcripts originate from the same promoter/enhancer regions
as the
pp24 and pp38 genes but are transcribed in the opposite
orientation
(
11,
22,
24,
88). Loss of oncogenicity and
altered
transcription have been associated with an expanded number
of 132-bp
repeats (4 to >35 units) within this 1.8-kb RNA region
(
10-12,
34,
61,
78,
90). Complex patterns of bidirectional
transcription,
which both initiate and terminate within the 132-bp
repeats, have been
previously reported (
22). Md5 contains a
single pair of
132-bp repeats located at nucleotide positions
12282 to 12546 and
129074 to 129338 (Fig.
1). This finding is
consistent with the number
of repeats (one to three copies) present
in other pathogenic MDV
strains (
11,
61,
78). Although there
are no readily
identifiable genes in this region based on our
criteria, there are four
ORFs of greater than 60 codons present.
Three of these ORFs have been
previously found in cDNA clones
(
41,
45,
71). We have
annotated the alternatively spliced
MDV006 and MDV075 genes based on
the work of Hong and Coussens
(
41), who identified a 14-kDa
protein from this region. Given
the complex transcriptional patterns
and alternate splicing which
occur within this region, additional
protein-coding sequences
which have not been annotated here may be
present (
12,
22,
41,
71).
Short repeats.
The short repeat regions are 12,264 bp at
nucleotide positions 141535 to 153798 and 164646 to 176909 and contain
12 genes (Fig. 1). The MDV084 and MDV100 genes encode homologues of the HSV-1 major immediate-early transactivating protein ICP4. These proteins, which contain 2,321 amino acids and comprise over 57% of the
short repeat regions, contain a 900-amino-acid amino-terminal extension
compared with ICP4 homologues of other herpesviruses. A similarly sized
ICP4 homologue is present in HVT and MDV1 GA (5, 107). Md5
encodes homologues of two additional immediate-early proteins found in
HSV-1: ICP27 (MDV068), which is essential for HSV-1 replication, and
ICP22 (MDV088). Md5 lacks homologues of immediate-early proteins ICP0,
which is nonessential for the replication of HSV-1 in cell culture, and
ICP47, a host range protein which blocks HSV-1 antigen presentation
(104).
The region containing the US/short repeat junction is variable in MDV1,
MDV2, and HVT (
14,
46,
106). Expansion of the
Md5 short
repeat compared to those of the MDV1 Md11 strain and
less-virulent JM
and Cu-2 strains has been previously noted by
restriction enzyme
analysis (
48). The MDV087 and MDV097 genes
span the US/short
repeat boundary (Fig.
1). The products of these
two genes have 119 identical amino-terminal amino acids that are
encoded within the short
repeat region. MDV087 was previously
described as SORF2 in MDV1 GA
(
14). Unlike MDV087, SORF2 is
encoded entirely within the US
region of MDV1 GA (
14). A homologue
of MDV097 is absent in
MDV1 GA. SORF2 has been shown to be nonessential
for replication of
MDV1 in cell culture, and it is absent in the
nonpathogenic MDV2
(
46,
69). MDV087 and MDV097 are similar
to putative proteins
from fowlpox virus and fowl adenovirus, suggesting
an avian host range
function for these proteins (
2,
14,
69,
86). Thus,
differences at the US/short repeat junction, including
the presence of
a second gene (encoding MDV097) similar to the
SORF2 gene, may affect
viral virulence and contribute to Md5's
enhanced
virulence.
A family of latency-associated transcripts (LATs) antisense to the ICP4
homologue has been described in MDV1 (
19,
20,
55,
56,
63).
Although the role of LATs in viral latency
and cell transformation is
poorly understood, a gene homologue
of the MDV086 and MDV098 genes has
been shown to encode a protein
from this region (
67). The
MDV083 and MDV101 genes also have
been annotated here as potential
genes. Given the complex splicing
of LAT transcripts within this
region, additional protein-coding
sequences may be
present.
Conclusions.
MDV1 genome analysis confirms the structural and
functional relatedness of MDV1 to other alphaherpesviruses in gene
complement and organization, particularly with regard to genes involved
in basic replicative functions. Novel DNA sequences in direct repeat regions and near unique/repeat junctions contain genes likely involved
in virulence and host range. The complete Md5 genome provides a basis
from which comparisons with MDV strains of lesser or greater virulence
may be made, thus contributing to our overall understanding of
pathogen-host interactions and the evolution of MDV virulence.
Additionally, this information will permit the engineering of novel
MDV1 vaccine viruses and expression vectors with enhanced efficiency
and greater versatility.
| |
ACKNOWLEDGMENTS |
We thank A. Ciupryk and G. Smoliga for excellent technical
assistance and W. H. Martinez, F. P. Horn, and R. G. Breeze for their interest and encouragement.
| |
FOOTNOTES |
*
Corresponding author. Mailing address: Plum Island
Animal Disease Center, P.O. Box 848, Greenport, NY 11944-0848. Phone:
(631) 323-3330. Fax: (631) 323-3044. E-mail:
gkutish{at}asrr.arsusda.gov.
| |
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Journal of Virology, September 2000, p. 7980-7988, Vol. 74, No. 17
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Abstract
Introduction
