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Research in Veterinary Science 85 (2008) 176–183


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Genetic characterization of Indian peste des petits ruminants


virus (PPRV) by sequencing and phylogenetic analysis of fusion
protein and nucleoprotein gene segments
N. Kerur a, M.K. Jhala a,*
, C.G. Joshi b

a
Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University,
Anand 388 001, Gujarat State, India
b
Department of Animal Genetics and Breeding, College of Veterinary Science and Animal Husbandry,
Anand Agricultural University, Anand 388 001, Gujarat State, India

Accepted 30 July 2007

Abstract

Peste des petits ruminants (PPR) is an important viral disease of sheep and goats, endemic in India. The study was undertaken to
characterize the local PPRV by sequencing fusion (F) protein and nucleoprotein (N) gene segments and phylogenetic analysis, so as
to focus on genetic variation in the field viruses. Selected regions of PPRV genome were amplified from clinical samples collected from
32 sheep and goats by RT-PCR and the resulting amplicons were sequenced for phylogenetic analysis. The phylogenetic tree based on the
322 bp F gene sequences of PPRV from five different locations clustered them into lineage 4 along with other Asian isolates. While the
425 bp N gene sequences revealed a different pattern of branching, yielding three distinct clusters for Nigerian, Turkey and Indian iso-
lates. Thus, classification of PPRV into lineages based on the N gene sequences appeared to yield better picture of molecular epidemi-
ology for PPRV.
Ó 2007 Elsevier Ltd. All rights reserved.

Keywords: Peste des petits ruminants virus; PPRV; F gene; N gene; Sequencing; Phylogeny

1. Introduction continent. However, in recent years, the disease has been


recorded in several parts of the world, Southern Asia
Peste des petits ruminants virus (PPRV), a member of including India, Pakistan and Nepal; Near East and the
the genus Morbillivirus in the family Paramyxoviridae Arabian Peninsula including Islamic Republic of Iran,
(Gibbs et al., 1979) is the causative agent of Peste des petits Iraq, Israel, Jordan, Kuwait, Lebanon, Oman, Saudi Ara-
ruminants (PPR), an acute viral disease of goats and sheep, bia, the United Arab Emirates and Yemen. In India, the
characterized by fever, erosive stomatitis, conjunctivitis, first outbreak of PPR was described by Shaila et al.
gastroenteritis and pneumonia. PPR is a highly contagious (1989), and since then, the disease has become endemic in
disease, morbidity and mortality can be as high as 100% India, causing severe economic losses and is presently con-
and 90%, respectively (Abu-Elzein et al., 1990). Following sidered as one of the major threats to about 200 million
the first report of the disease in sheep and goats (Gargaden- small ruminant population of the country.
nec and Lalanne, 1942), for many years it was believed to PPR can be confused clinically with rinderpest, and
have remained restricted to western part of the African hence the clinical observations for both the diseases should
always be confirmed by a laboratory test. The diagnostic
*
Corresponding author. Tel.: +91 2692 261505; fax: +91 2692 261201. techniques used in the past viz. VNT, AGID and isolation
E-mail address: mkjhala_2003@yahoo.co.in (M.K. Jhala). of the virus in cell culture are time consuming and labour

0034-5288/$ - see front matter Ó 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.rvsc.2007.07.007
N. Kerur et al. / Research in Veterinary Science 85 (2008) 176–183 177

intensive. With the advent of molecular biological tech- 2.3. RT-PCR for PPRV detection
niques like PCR, rapid and specific diagnosis of PPR has
become possible (Forsyth and Barrett, 1995; Couacy- RNA was extracted from the clinical samples (100 mg
Hymann et al., 2002). tissue), reference vaccine virus (250 ll) and a blood sample
PPRV is genetically grouped into four distinct lineages (200 ll) from an apparently healthy goat, using TRI
(1, 2, 3 and 4) on the basis of partial sequence analysis of ReagentÒ (Sigma–Aldrich), as per the modified method
fusion protein (F) gene; despite the fact that only a single of guanidium thiocyanate-phenol-chloroform extraction
serotype of PPRV has been reported (Shaila et al., 1996; method originally described by Chomczynski and Sacchi
Dhar et al., 2002; Ozkul et al., 2002). This classification (1987), and the RNA was resuspended in 20 ll of nuclease
of PPRV into lineages has broadened our understanding free distilled water. Five microliters of the extracted RNA
of the molecular epidemiology and worldwide movement was reverse transcribed using Omniscriptä Reverse Trans-
of PPR viruses. However, continuing increase in circula- criptase Kit (QIAGEN, Germany). The reaction was car-
tion of the virus among the susceptible population in ende- ried out in 200 ll tubes with the following conditions:
mic countries like India, a demand was felt to delve into the 1 ll of random hexamer, 0.125 mM each dNTPs, 10 units
molecular details of the field virus. The objectives of our of ribonuclease inhibitor (MBI Fermentas), two units of
research were to detect the PPRV in suspected outbreaks OmniscriptÒ reverse transcriptase and the buffer provided
of PPR among sheep and goats of Gujarat (a western state by the manufacturer in a total volume of 20 ll. The reac-
of India), by employing F gene based primers described by tion was carried out at 37 °C for 60 min and stopped by
Forsyth and Barrett (1995). In addition, a new pair of incubation at 95 °C for 10 min.
nucleoprotein (N) gene based primers was developed for Three microliters of the RT product was used as tem-
specific and sensitive detection of PPRV from clinical sam- plate for the PCR, carried out in 200 ll thin walled PCR
ples. Further, the genetic relationships between these tubes, in a final reaction volume of 25 ll with following
viruses were investigated comparing the nucleotide reagents: 12.5 ll of PCR Master mix (MBI Fermentas)
sequences of the PCR products amplified from F and N containing 0.05U/ll TaqDNA polymerase (recombinant)
genes with other PPRV sequences available in GenBank in reaction buffer, MgCl2 (4 mM) and dNTPS (0.4 mM of
of National Center for Biotechnology Information each), 1 ll of forward and reverse primers (10 pmoles of
(NCBI). each primer) and 7.5 ll of deionized water. In case of F1/
F2 primers, 35 cycles of amplification was carried out using
2. Materials and methods PCR reaction conditions as described by Dhar et al. (2002).
The reaction conditions for N1/N2 primers were as fol-
2.1. Clinical samples and reference virus lows: 94 °C for 10 min, followed by 35 cycles at 94 °C for
30 s, 50 °C for 30 s and 72 °C for 45 s, and a final extension
Blood, nasal swabs, spleen and lymph node samples step at 72 °C for 10 min. Ten microliters of the PCR prod-
from 32 sheep and goats with symptoms suggestive of ucts were resolved on a 2% agarose gel stained with 0.5 lg/
PPRV infection were collected. A total of 48 clinical sam- ml ethidium bromide.
ples from five outbreaks at different locations (Anand,
Mehsana, Banaskantha, Patan and Rajkot districts) in 2.4. Cloning and sequencing of PCR products
Gujarat were collected. A representative sample from each
district was subsequently taken for sequencing work, where The PCR products (a representative sample from each
the samples from Anand, Mehsana and Banaskantha were location) specific to F and N genes of PPRV amplified
from goats, while the same from Patan and Rajkot districts using the primer pairs F1/F2 and N1/N2, respectively,
were from sheep. Lyophilized freeze-dried live PPR vaccine were ligated into pTZ57R/T vector supplied with InsT/
(Sungri isolate) obtained from the Division of Virology, Acloneä PCR product cloning kit (MBI Fermentas) fol-
IVRI, Mukteswar, India, was used as the reference virus lowing the manufacturer’s instructions. Three microliters
during the course of study. of ligation product was used to transform Escherichia coli
DH5-a made competent, as per the method described by
2.2. Oligonucleotide primers Sambrook and Russel (2001). The bacteria containing the
recombinant plasmids were screened by standard aplha
The random hexamers used for cDNA synthesis and the complementation method using X-gal and IPTG on LB
primers F1/F2 and N1/N2 used were obtained from Sigma agar plates containing ampicillin (50 lg/ml). The white col-
Genosys and MWG-Biotech AG, Germany. The primers onies containing desired inserts were screened by colony
N1/N2 amplifying a region of N gene were designed in PCR using previously described conditions for each set of
house using the software GeneFisher 1.2 available online primers. The bacterial colonies containing desired insert
(http://bibiserv.techfak.uni-bielefeld.de/genefisher/), based were cultured in LB broth containing appropriate antibi-
on the published sequence information (accession Nos. otic and the recombinant plasmid was purified from 3 ml
AJ563705, AY560591, X74443 and AJ849636). Details of of culture using QIAprepÒ Spin Miniprep Kit (QIAGEN,
the primers are listed in Table 1. Germany) following manufacturer’s instructions. The pres-
178 N. Kerur et al. / Research in Veterinary Science 85 (2008) 176–183

Table 1
Details of the primers used for detecting PPRV by PCR
Sr. no. Primer Primer sequence Target gene Expected amplicon Reference
and position size
1 F1 (F) 50 ATC ACA GTG TTA AAG CCT GTA GAG G 3 0 F gene 777-801 372 bp Forsyth and Barrett (1995)
2 F2 (R) 50 GAG ACT GAG TTT GTG ACC TAC AAG C 3 0 F gene 1124-1148
3 N1 (F) 50 GAT GGT CAG AAG ATC TGC A 3 0 N gene 1208-1226a 463 bp Designed during the
4 N2 (R) 50 CTT GTC GTT GTA GAC CTG A 3 0 N gene 1670-1652a experiment
a
Position of the primers is as per the numbering of Genbank sequence X74443.

ence of appropriate insert was once again confirmed by car- including 13 blood, 10 nasal swab and one spleen samples
rying out PCR using the purified recombinant plasmid as as well as the blood sample taken from apparently healthy
template. The inserts in the recombinant plasmids were goat failed to produce the targeted amplification.
sequenced by cycle sequencing using ABI PRISMÒ 310 A total of 18 representative samples, half of which were
Genetic Analyzer (Applied Biosystems, USA) and Big- negative and the other half positive by F gene based RT-
DyeÒ Terminator v3.1 Cycle sequencing kit (Applied Bio- PCR, were selected for detection of PPRV by the newly
systems, USA). designed primers N1/N2. Care was taken to include at least
two samples from each of the five locations (Anand, Meh-
2.5. Sequence analyses sana, Banaskantha, Patan and Rajkot districts). Primers
N1/N2 could produce the desired amplicons (463 bp) in
The nucleotide sequences of 322 bp and 425 bp seg- 12 of the 18 samples tested.
ments amplified from F and N genes, respectively were
aligned with corresponding sequences available in Gen- 3.2. Sequence analyses
Bank using Clustal W (Thompson et al., 1994). Phyloge-
netic analysis of F and N gene segments of PPRV was The analysis of the 322 bp F gene sequences (accession
performed with the DNADIST and FITCH programmes Nos. DQ267183, DQ267184, DQ267185, DQ267186,
of PHYLIP 3.65 software (Felsenstein, 1989). The phylo- DQ267187) revealed that, the homology among the five
genetic tree was generated as follows: A set of 500 aligned field isolates (Ana/Guj/05, Ptn/Guj/05, Meh/Guj/05, Bsk/
sequences was generated by the bootstrap method (Seq- Guj/05 and Rjk/Guj/05) of present study ranged between
boot programme). Genetic distances were calculated for 96% (for Bsk/Guj/05 and Ptn/Guj/05) and 99% (for Ana/
each set of aligned sequence with the DNADIST pro- Guj/05 and Rjk/Guj/05). None of the field isolates had
gramme, and the trees were constructed by the FITCH homology less than 96% with any of the Indian isolates
programme using corresponding sequence of Rinderpest described previously. Further, none of the field isolates
virus (RPV) as an out group. Finally, the consensus tree had identities less than 97% with the reference vaccine virus
for 29 (F gene sequences) and nine (N gene) sequences sequenced. All the field isolates and vaccine virus shared
of representative isolates was generated using the Con- comparatively lesser homology (92–93%) with the Nigerian
sense programme. isolate Nigeria/75/1.
Further, Phylogenetic network analysis was carried out Similarly, analysis of 425 bp sequences of N gene (acces-
using the software Network 4.111 (available for download sion Nos. DQ267188, DQ267189, DQ267190, DQ267191,
from website www.fluxus-engineering.com). Both F and N DQ267192) of field PPRV isolates (Ana/Guj/05, Ptn/Guj/
gene sequence data were processed by star contraction 05, Meh/Guj/05, Bsk/Guj/05 and Rjk/Guj/05) revealed
algorithm (Forster et al., 2001), followed by processing that all the isolates from the present study and Indian iso-
with median-joining (MJ) network algorithm (Bandelt lates described earlier were closely related to each other
et al., 1999) to draw separate phylogenetic network for with sequence identity of 98–99%. Homology of all the field
each gene sequence, depicting the points of variation isolates with Nigeria/75/1, isolates of Turkey (Turkey-2000
among the sequences under comparison. and Turkey/00) and Sungri/96 ranged between 88–89%,
94–95% and 98–99%, respectively.
3. Results The Phylogenetic tree (Fig. 1) based on the 322 bp
sequence of F gene clustered all the isolates of India includ-
3.1. Detection of PPRV by F and N gene based RT-PCR ing the isolates from the present study, isolates of turkey,
an isolate of Pakistan and Iran into a separate branch from
Amplification with primers F1/F2 yielded an expected Nigerian isolate. While the Phylogenetic tree based on the
amplicon of 372 bp in reference vaccine virus as well as 425 bp N gene sequences out-rooted the Nigerian isolate,
24 (50.00%) samples consisting of 12 blood, 11 nasal swabs while the Turkey and Indian isolates were grouped into
and one lymph node. The remaining 24 (50.00%) samples two clusters, although with low bootstrap values (Fig. 2).
N. Kerur et al. / Research in Veterinary Science 85 (2008) 176–183 179

Fig. 1. Phylogenetic relationship of PPRVs of Gujarat to other virus isolates, based on the 322 bp partial sequence of fusion (F) protein gene. All the
Asian isolates (lineage 4) including the isolates from the present study clustered into a separate branch from the Nigerian isolate. The lone isolate Bsk/Guj/
05 clustered (C2) with previously described kcch2000 isolate, while the other four isolates clustered along with vaccine virus in C1.

The network analysis based on 322 bp F gene sequences Ana//Guj/05, Meh/Guj/05 and Ptn/Guj/05 showed, three,
resulted in a large central node URI99 on the torso, with three and two mutations, respectively disregarding the
three identical isolates Uri99, Izat94 and Sung96 in it torso.
(Fig. 3). The torso was formed by central node URI99 Similarly, the Network analysis for the 425 bp sequence
and LAXM99. Izat98 along with Chirg98 formed a second of N gene showed the isolate Bsk/Guj/05 in the torso
node (IZAT98), outside the torso. The five isolates of the (Fig. 4) and the four other isolates of the present study
present study differentiated into five minor taxa. The iso- showed comparatively fewer mutations disregarding the
late Rjk/Guj/05 was the closest to the central node torso. Among the isolates of Gujarat, comparatively more
URI99 with a single mutation (at position 263) disregard- number of mutations (4) were seen in Meh/Guj/05, while
ing the torso. The isolate of Banaskantha district (Bsk/ the isolate Rjk/Guj/05 showed only one mutation. The iso-
Guj/05) with six mutations was the most distant taxon lates Sungri/96, Ana//Guj/05 and Ptn//Guj/05 showed two
from the central node. The other isolates of Gujarat, mutations each.
180 N. Kerur et al. / Research in Veterinary Science 85 (2008) 176–183

2003–04). The same report has also detailed one outbreak


in sheep of Banaskantha district (northern part of Guja-
rat), where eight animals died in 2002. No incidence was
reported earlier from Anand (central Gujarat), Mehsana
and Patan districts (both in northern Gujarat). However,
incidences in seven other districts belonging to northern,
central and western parts of Gujarat, with one or two out-
breaks were reported from 1996 to 2002. The majority of
these outbreaks occurred between November and February
(winter months), and a few in March and April. This shows
that PPR outbreaks did not occur every month, but they
appeared every year in Gujarat state, making the disease
endemic.
Recently, there have been a couple of attempts with
promising results, targeting N gene for PCR based detec-
tion of PPRV (Couacy-Hymann et al., 2002; George,
2002). The N gene based primers, despite being proved to
offer higher sensitivity, they are yet to gain wide acceptance
for the diagnosis of PPRV. The primer pair N1/N2 was
designed in-house based on the published sequences in
Genbank. N gene codes for an internal structural protein
and also mRNAs of N gene are the most abundant tran-
scripts of the virus, making it attractive target for develop-
ment of a highly sensitive diagnostic assay. Indeed, due to
lack of proof reading function of their polymerases, RNA
viruses are known to contain high rate of nucleotide substi-
tution error frequency (Steinhauer and Holland, 1986).
Therefore, to ensure efficient amplification and detection
of such viruses, the primers have to be designed by identi-
fying conserved region in the published sequences of the
viral isolates from different geographical region; this strat-
egy minimizes the risk of false negative result due to primer
template mismatch. In order to design PCR primers that
Fig. 2. Phylogenetic relationship of PPRVs of Gujarat to other virus would selectively amplify PPRV genome without cross
isolates, based on the 425 bp partial sequence of nucleoprotein (N) gene.
reacting with RPV, the N gene sequences of PPRV and
C1, C2 and C3 clusters include the isolates from Nigeria, Turkey and
India, respectively, showing better geographical localization of the RPV available in the Genbank were aligned with Clustal
isolates. W software to identify a region unique to PPRV among
all PPRV strains. Hence, the terminal 1/3rd region of
PPRV mRNA at 3 0 end, which shares low homology with
4. Discussion other Morbilliviruses (Diallo et al., 1994) was chosen as a
target for designing the primers. The alignment of N1/N2
The F gene based RT-PCR developed by Forsyth and with PPRV N gene sequences showed 100% homology in
Barrett (1995) has gained much popularity, though PCR all the strains, except for a mismatch at positions 4 base
based on other gene targets have become available only from 3 0 end of N1 in case of Sungri/96 (accession No.
recently. The PPR specific primers F1 and F2 developed AY560591) strain. Whereas, the alignment with N2 showed
by aforementioned workers give an amplification of a one mismatch at position 15 from 3 0 end in case of Nigeria/
372 bp region between positions 777 to 1148 nucleotides 75/1 (accession No. X74443). Both the primers (N1and N2)
of PPRV F gene. In the present study, PPRV could be satisfied the minimal homology requirement for PCR, as
detected in 24 (50%) of the 48 clinical samples tested, which defined by Sommer and Tautz (1989), i.e. the first three
confirmed PPRV in all the five outbreaks at different loca- nucleotides at the 3 0 ends are conserved in all the N gene
tions, with highest number (18) of animals affected in sequences of PPRV available to date in Genbank. The
Northern Gujarat region. available sequences were from four different strains, Nige-
Although, the complete history of the current PPR out- ria/75/1, Sungri/96, Turkey2000 and Turkey/00. The align-
breaks were not available, there were reports of six PPR ment of primers N1/N2 shows sufficient mismatches with
outbreaks in Rajkot district (western part of Gujarat) in RPV ensuring that they do not amplify the RPV genome.
1997–98, where 545 animals (both sheep and goats) were Primers N1/N2 detected PPRV in a greater number of
affected, of which, 400 died (ADMAS Annual Report, samples than F gene based primers. Three samples negative
N. Kerur et al. / Research in Veterinary Science 85 (2008) 176–183 181

Fig. 3. Phylogenetic network analysis based on the partial fusion (F) protein gene sequence of field PPRVs with corresponding sequences published in
GenBank. The five isolates from the present study differentiated into five minor taxa showing mutations ranging from one to six. The Nigerian isolate
showed maximum number (18) of mutations.

Fig. 4. Phylogenetic network analysis based on the partial nucleoprotein (N) gene sequence of field PPRVs with corresponding sequences published in
GenBank, showing the isolate Bsk/Guj/05 in the torso. The other four isolates of the present study showed one to four mutations. Isolates from Turkey
and Nigeria varied greatly with 18 and 48 mutations, respectively.

by F gene based RT-PCR were positive by N gene based the N gene based primers were more sensitive than F gene
RT-PCR, however, no sample positive by F gene based based primers. The higher sensitivity of N1/N2 can be
RT-PCR was negative by N gene based RT-PCR. Thus, attributed to abundance of PPRV N gene transcripts than
182 N. Kerur et al. / Research in Veterinary Science 85 (2008) 176–183

Table 2
Sequence identity of partial F and N gene sequences between isolates of different geographical locations
Sr. no Geographical location Sequence identity
F gene N gene
1 Indian isolate (lineage 4) Turkey isolates (lineage 4) 96–98% 94–95%
2 Indian isolate (lineage 4) Nigerian isolate (lineage 1) 92–93% 88–89%
3 Turkey isolates (lineage 4) Nigerian isolate (lineage 1) 92% 90%
4 Indian isolate (lineage 4) Indian isolate (lineage 4) 96–99% 98–99%
5 Turkey isolates (lineage 4) Turkey isolates (lineage 4) 98% 99%

the F gene (Ghosh et al., 1995), thus making N gene suit- on the 322 bp F gene and 425 bp N gene segments by Net-
able target for improving the sensitivity of RT-PCR for work 4.111 software, allowed identification of the number
detection of PPRV from clinical samples. and position of the variation in the nucleotide sequences
To assess the genetic similarity and divergence among by depicting the varying position in each sequence in a pic-
the field PPRVs of Gujarat as well as their relatedness to torial format. Further, network analysis clustered the iden-
some of the previously described isolates, the partial F tical isolates into nodes and non-identical isolates formed
and N gene sequence data were analysed in silico by separate taxa branching from the central torso.
employing software tools viz. Clustal W, PHYLIP and In summary, relative to the conventional F gene target,
Network 4.111. Sequence analysis of F and N gene the N gene target offered better sensitivity for detection of
sequence data revealed that the PPRVs from distant geo- PPRV from clinical samples. The newly designed primers
graphical regions vary to a greater extent in their N gene N1/N2 proved to be more efficient for this purpose and
sequences than in their F gene sequences (Table 2). can be used widely in PCR diagnosis of PPR. The partial
A consensus Phylogenetic tree based on the lineage spe- F gene sequence based classification of PPRV into lineages
cific 322 bp F gene sequence was constructed with help of placed the local isolates into lineage 4. Classification of
PHYLIP programmes. In accordance with the previous PPRV into different lineages based on N gene sequence
studies (Shaila et al., 1996; Dhar et al., 2002; Ozkul appeared to group the viruses in a better way, thus, giving
et al., 2002), all the Asian isolates including the isolates better epidemiological picture about PPRV. However,
of turkey, clustered together into a separate branch from given the ability for PPRV to mutate, it is desirable to have
the Nigerian isolate, and the branching was supported by more than one set of primer for diagnosis and F and N
a bootstrap values of 500 (100%). Since the sequence data genes are the most suitable candidates.
for the African isolates belonging to lineages 2 and 3 were
not available in the Genbank, they were not included in the Acknowledgement
Phylogenetic analysis. Thus, from the Phylogenetic tree
(Fig. 1), it is evident that all the isolates of Gujarat clus- The authors are thankful to Dr. R.K. Singh, Head,
tered together with the other Asian isolates of lineage 4. Division of Virology, IVRI, Mukteswar, India, for provid-
Similarly, a Phylogenetic tree (Fig. 2) was generated for ing PPR vaccine.
the 425 bp sequence of N gene, which clustered the Nige-
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