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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
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
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
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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