Content uploaded by Dieter Klein
Author content
All content in this area was uploaded by Dieter Klein on Jul 27, 2016
Content may be subject to copyright.
Downloaded from www.microbiologyresearch.org by
IP: 104.249.141.27
On: Wed, 27 Jul 2016 20:44:44
Short
Communication
Phylogenetic analysis of feline immunodeficiency
virus in Central Europe: a prerequisite for
vaccination and molecular diagnostics
Adolf Steinrigl and Dieter Klein
Correspondence
Dieter Klein
dieter.klein@vu-wien.ac.at
Institute of Virology, University of Veterinary Medicine, Veterina¨rplatz 1, A-1210 Vienna, Austria
Received 29 July 2002
Accepted 23 December 2002
Feline immunodeficiency virus (FIV) is a worldwide-occurring lentivirus that severely impairs the
immune function of infected domestic cats. Due to structural and biological similarities, FIV
represents a promising model for human immunodeficiency virus (HIV) and AIDS. A major obstacle
in developing vaccines against lentiviruses is their high mutation rate. Furthermore, mutations in
target sequences provide a pitfall for molecular diagnostics. It is therefore important to determine
the genetic diversity of lentiviruses in any region where vaccination or implementation of new
diagnostic techniques are planned. This study presents a phylogenetic analysis of 30 FIV strains
derived from Central Europe. In order to improve the reliability of genotyping, DNA from two different
proviral genes was amplified and comparative phylogenetic trees were inferred. The highly
coincident results point to the existence of extensive virus variation with the presence of at least
two highly divergent subtypes of FIV in Austria and Germany.
Feline immunodeficiency virus (FIV) is a commonly
occurring lentivirus able to establish persistent infections
in domestic cats (Bendinelli et al., 1995). As with human
immunodeficiency virus (HIV), several genetically distinct
subtypes (clades A–E) have been reported, revealing up
to 26 % sequence diversity among parts of the env genes
(Sodora et al., 1994; Kakinuma et al., 1995; Pecoraro et al.,
1996). Infection finally leads to a debilitating disease that
resembles AIDS in humans: after a variably long clinical
latency period, infected hosts become susceptible to second-
ary and opportunistic infections or develop tumours, which
are rarely seen otherwise (Pedersen et al., 1989; English et al.,
1994). Consequently, several attempts have been made to
develop a vaccine against FIV infection using different
strategies (Yamamoto et al., 1993; Hosie et al., 1995, 1998;
Matteucci et al., 1996; Lockridge et al., 2000; Bigornia
et al., 2001; Pu et al., 2001). Several single-subtype vaccines
protected against challenge with homologous or slightly
heterologous virus but failed to protect against more
distantly related strains (Elyar et al., 1997). In contrast, a
double-subtype virus vaccine has been proven to elicit
considerable protection against challenge with virus of a
third subtype, not included in the vaccine (Pu et al., 2001).
This vaccine has now been approved by the USDA; however,
its efficacy still remains to be shown under field conditions
(Uhl et al., 2002).
As the success of a vaccine could be hampered by the occur-
rence of highly divergent virus variants, the genetic diversity
of FIV field strains circulating in all regions where vac-
cination is planned should be determined (Pistello et al.,
1997). This knowledge should also allow the adaptation of
vaccines to regionally prevalent subtypes, if development
of a ‘global’ FIV vaccine should be impossible.
The extensive genetic variation observed in FIV also has a
direct impact on PCR-based methods which are increas-
ingly used for diagnosis and monitoring of FIV infection
(Leutenegger et al., 1999; Hosie et al., 2002). Furthermore,
PCR assays to distinguish vaccinated from infected cats
will gain importance with the advent of the first commer-
cially available FIV vaccine (Uhl et al., 2002). In general,
these methods are highly influenced by variations in the
target sequences, which usually increase with genetic
distance (Klein et al., 1999, 2001).
To gain insight into the genetic diversity of FIV in Central
Europe, we sampled EDTA-blood from 30 FIV-positive
domestic cats derived from Austria, Germany, Switzerland
and Italy. FIV infection was initially determined by PCR
and in 27 of 30 cases additionally by ELISA (Table 1). Partial
proviral gag and env genes were amplified with primers
FIV-1026F (59-GGC ATA TCC TAT TCA AAC AG-39) and
FIV-1700R (59-AAG AGT TGC ATT TTA TAT CC-39)
(Cammarota et al., 1996) for gag, and FIV-7316F (59-ATA
CCA AAA TGT GGA TGG TG-39) and FIV-7868R (59-TGC
AAG ACC AAT TTC CAG CA-39) for env (sequences kindly
provided by M. Pistello, University of Pisa, Italy). The env
Sequences reported in this study are deposited under the GenBank
accession numbers: AF531031 – AF531076 and AY196330 – AY196343.
0001-8736 G2003 SGM Printed in Great Britain 1301
Journal of General Virology (2003), 84, 1301–1307 DOI 10.1099/vir.0.18736-0
Downloaded from www.microbiologyresearch.org by
IP: 104.249.141.27
On: Wed, 27 Jul 2016 20:44:44
sequences of samples DEBAd59 and ATNOd16 were
amplified by nested PCR using FIV-7224F (59-GTA CAG
ACC CAT TAC AAA TC-39) and FIV-8000R (59-CTG CCA
CTG GGT TAT ACC AA-39) as outer and FIV-7316F/FIV-
7868R as inner primers. After purification, the amplicons
were directly sequenced on both strands, using PCR
primers. In the case of strain DEFRd68, repeated PCR and
sequencing experiments did not result in a clean sequence.
Therefore, the PCR product was cloned into a commercial
vector (TA Cloning kit; Invitrogen) and six positive clones
were sequenced. The clonal sequences varied by a P-value
of 0–1?3 % sequence diversity (for comparison, the seq-
uence closest to these clones differed from them by 4?9–
5?7 % sequence diversity). Finally, a consensus sequence
for DEFRd68 was derived which was used for phylo-
genetic analysis.
Both gag and env data sets were compiled using reference
strains from GenBank. In order to compare the gag and env
topologies under the same conditions, we used only those
reference strains from GenBank where both corresponding
gene regions were available. Several Japanese strains
reported as being likely recombinants of different subtypes
within the env region investigated in this study (Carpenter
et al., 1998) were excluded from analysis. Sequences
described as subtype E (Pecoraro et al., 1996) overlapped
with the Central European sequences only along a stretch
of 288 nt in gag and were likewise excluded. Multiple
alignments were created with CLUSTAL X (Thompson et al.,
1997) and edited with DAMBE (Xia & Xie, 2001), resulting in
a 562 nt gag and a 504 nt env alignment.
To estimate the phylogenetic signal contained in the gag
Table 1. Summary of all Central European FIV strains reported in this study
The countries of origin and provinces of FIV-infected cats are given. Results of serological testing and genotyping are indicated. The NCBI
accession numbers are also given. ND, Not determined; +, positive ELISA result.
Strain Country Province Serology
Subtyping GenBank
gag env gag env
ATVIa33 Austria Vienna ND B B AF531056 AF531045
ATVIa85 Austria Vienna ND B B AF531061 AF531040
ATVIa90 Austria Vienna +B B AF531059 AF531036
ATESb20 Austria Spain*/Vorarlberg +B B AF531049 AF531032
ATSTb30 Austria Styria +B B AF531054 AF531046
ATVIb31 Austria Vienna ND B B AF531063 AF531031
ATVIb97 Austria Vienna +B B AF531055 AF531042
ATSTc01 Austria Styria +B B AF531058 AY196341
ATNOc07 Austria Lower Austria +B B AY196330 AY196336
ATNOd01 Austria Lower Austria +B B AF531060 AY196332
ATVId02 Austria Vienna +A A AF531075 AF531047
ATESd03 Austria Teneriffa*/Vienna +B B AF531050 AY196331
ATVId05 Austria Vienna +B B AF531062 AY196335
ATVId06 Austria Vienna +B B AF531065 AY196334
ATNOd16 Austria Lower Austria +B B AF531057 AY196342
ATVId20 Austria Vienna +B B AF531064 AY196333
ATVId23 Austria Vienna +B B AF531066 AY196337
DEBWa06 Germany B.-Wu
¨rttemberg +B B AF531048 AF531044
DEBAb91 Germany Bavaria +A A AF531069 AF531043
DEBAd58 Germany Bavaria +A A AF531070 AF531037
DEBAd59 Germany Bavaria +A A AF531074 AY196343
DENWd60 Germany N.-Westfalen +A A AF531072 AY196340
DEBAd65 Germany Bavaria +A A AF531068 AY196338
DEFRd68 Germany France*/Bavaria +A A AF531071 AY196339
DENWd70 Germany N.-Westfalen +A A AF531073 AF531038
DEBEd72 Germany Berlin +B B AF531051 AF531039
CHTGa05 Switzerland Thurgau +A A AF531076 AF531034
CHSHa10 Switzerland Schaffhausen +A A AF531067 AF531033
ITROd76 Italy Rome +B B AF531052 AF531035
ITROd78 Italy Rome +B B AF531053 AF531041
*These strains were isolated from cats living in Austria and Germany, but coming originally from Spain or France.
1302 Journal of General Virology 84
A. Steinrigl and D. Klein
Downloaded from www.microbiologyresearch.org by
IP: 104.249.141.27
On: Wed, 27 Jul 2016 20:44:44
and env alignments, likelihood mapping (Strimmer &
von Haeseler, 1997) was performed using TREE-PUZZLE
(Strimmer & von Haeseler, 1996). With this method, the
percentage of completely resolved quartet trees from a
representative fraction of all possible quartets in a data set
can be taken as a measure for the phylogenetic signal
contained in an alignment. As a result, both alignments
appeared to be highly informative, revealing 87?0% in
env and 86?6% in gag of all analysed quartets being
completely resolved.
As none of the most commonly used models for phylo-
genetic inference is principally superior to the others (Graur
& Li, 2000), distance (Saitou & Nei, 1987), parsimony
(Fitch, 1977) and maximum-likelihood (Felsenstein, 1981;
Strimmer & von Haeseler 1996) analyses were performed for
phylogenetic tree construction. To determine the substitu-
tion models that would best fit our data sets for maximum-
likelihood and neighbour-joining analyses, a likelihood
ratio test (Swofford et al., 1996) was performed using PAUP*
(version 4.0b10; Swofford, 2002). In the gag alignment,
the Tamura–Nei model (Tamura & Nei, 1993) with gamma-
distributed rates (TN93+C) resulted in a likelihood esti-
mate not significantly worse than the general time reversible
model with estimated gamma-distribution and proportion
of invariant sites (GTR+C+I), which is the most com-
plicated model implicated in the program. In contrast, the
likelihood ratio test favoured a submodel of the GTR+C+I
model in env with three different substitution rates: one for
both possible transitions, one for three of the four possible
transversions and one for A«C changes. Consequently, the
TN93+Cmodel was used to construct quartet puzzling
trees (Strimmer & von Haeseler, 1996) as well as neighbour-
joining trees (Saitou & Nei, 1987) based on the gag align-
ment, whereas the same tree-building algorithms were
used, assuming the special GTR+C+I model for the env
alignment. Parsimony analyses were performed on both
data sets using the heuristic search algorithm. All described
tree constructions were performed using PAUP*, and MEGA
2.1 (Kumar et al., 2001) was used to calculate neighbour-
joining trees.
The tree topologies resulting from the different calculations
were highly similar within each data set. Representative
maximum-likelihood trees (Fig. 1) and neighbour-joining
trees (Fig. 2) are shown. Upon comparison, trees derived
from the different proviral regions investigated showed
highly concordant topologies (Figs 1 and 2). All Central
European sequences reported in this paper grouped into
either subtype A or B of FIV. Within clade B, several sub-
clades were consistently observed among both data sets.
According to the origin of the virus strains, we termed these
subclades B-main, Austria-1, Austria-2, Austria-3 and
Portugal. A single Austrian strain (ATVId23) did not fall
into either of these subgroups and might represent a proto-
type of another subclade of subtype B, as is suggested by the
long branch that separates it from the other strains. Only
two Austrian strains (ATESb20 and ATESd03) cluster with
B-main. Interestingly, both of them were isolated from
cats which, according to the owners, were born in Spain
but were taken to Austria later in their life (Table 1). The
close proximity of these strains is especially intriguing, based
on the fact that the samples were collected at different time
points in distinct parts of Austria. Moreover, they displayed
reasonable diversity from all other Austrian sequences, as
they grouped with cluster B-main. Therefore, we consider
it very likely that both cats had actually been infected in
Spain. Unfortunately, there are no Spanish FIV-sequences
available, and thus comparison with Spanish strains was
not possible. Both Italian strains reported here (ITROd76
and ITROd78) were grouped together extremely closely as
well, but in this case close epidemiological linkage is very
likely as both samples are derived from a population of
feral cats in Rome. The occurrence of subtype B strains
of FIV in Germany has been suggested by heteroduplex
mobility analysis (Bachmann et al., 1997). Accordingly, two
German strains (DEBWa06 and DEBEd72) fell into this
subtype. All other German FIV strains belonged to subtype
A, together with both Swiss sequences and a single Austrian
strain. Formation of a highly supported subclade (Germany-
1) consisting of two German strains was observed in subtype
A. In gag but not in env, the single Austrian clade A strain
ATVId02 also grouped to this cluster.
As stated above, the trees inferred from gag and env regions
were highly similar. However, there were some interesting
discrepancies: strain DEBEd72 and the US-Maryland strain
both grouped to B-main in gag, but were clearly separated
from this subclade in env. Surprisingly, the US-Maryland
strain clustered close to or within subclade Austria-2 in env,
supported by high quartet puzzling and bootstrap values
(Figs 1 and 2).
Moreover, a separation of clade B from clades C and D was
not supported in neighbour-joining analyses of the env
data (Fig. 2b). To test whether inter-subtype recombina-
tion could be the reason for this observation as well as
for the discordant grouping of DEBEd72 and Maryland
strains, gag and env sequences were concatenated, and boot-
scanning (Salminen et al., 1995) was performed using SIMPLOT
(Lole et al., 1999). USIL2489_7B, Petaluma, BM3070 and
Shizuoka served as reference sequences for the four subtypes
included. However, no significant signs of recombination
were observed among our data. In the absence of recombina-
tion and significant differences in phylogenetic content, the
observed discrepancies might be due to the different evolu-
tionary constraints effective on the gag and env genes,
respectively (Pistello et al., 1997; Rigby et al., 1993). In the
presented data sets, roughly 90 % of substitutions occurring in
gag were estimated to be synonymous in comparison to about
50 % synonymous substitutions in env. Synonymous sub-
stitutions are generally believed to better display the true
evolutionary history, as they are theoretically not influenced
byselectivepressure(Graur&Li,2000).Thepositiveselection
pressure on env might account for the observed differences
in our data. However, a detailed description of FIV phylogeny
http://vir.sgmjournals.org 1303
Phylogenetic analysis of FIV
Downloaded from www.microbiologyresearch.org by
IP: 104.249.141.27
On: Wed, 27 Jul 2016 20:44:44
Fig. 1. Maximum-likelihood trees constructed by quartet puzzling. Numbers above the branches indicate the percentage of 1000 puzzling steps. Puzzle support values
above 70 % are shown. Branch lengths are drawn to the scale at the bottom of each tree. The major subtypes A, B, C and D, as well as subclades of subtypes A and B, are
indicated. Trees are midpoint-rooted. (a) Tree inferred from the 562 nt gag alignment. Reference sequences (GenBank): USIL2489_7B (U11820), ItalyM2 (Y13867),
ItalyM3 (Y13866), Sendai2 (D37821), TM2 (M59418), Maryland (AF361320), Aomori2 (D37824), PP2 (AJ304959), RP1 (AJ304962), Shizuoka (D37818), Fukuoka
(D37822), BM3070 (AF474246), Petaluma (M25381), FIV_Wo (L06135), FIV_PPR (M36968), Sendai1 (D37820) and FIV_113 (X68019). (b) Tree inferred from the
504 nt env alignment. Reference sequences were: ItalyM2 (X69501), ItalyM3 (X69502), Aomori2 (D37817), Sendai2 (D37814), Maryland (AF452126), PP2 (AJ304985),
RP1 (AJ304988), Shizuoka (D37811), Fukuoka (D37815), FIV_Wo (L06135), FIV_113 (X60725) and Sendai1 (D37813). For accession numbers for Petaluma, FIV_PPR,
USIL2489_7B, TM2 and BM3070 see (a).
1304 Journal of General Virology 84
A. Steinrigl and D. Klein
Downloaded from www.microbiologyresearch.org by
IP: 104.249.141.27
On: Wed, 27 Jul 2016 20:44:44
Fig. 2. Unrooted neighbour-joining trees. Numbers next to the branches indicate the percentage of 1000 bootstrap replicates. Bootstrap values above 80 % are shown.
Branch lengths are drawn to the scale at the bottom of each tree. The major subtypes A, B, C and D, as well as subclades of subtypes A and B, are indicated. (a) Tree inferred
from the 562 nt gag alignment. (b) Tree inferred from the 504 nt env alignment. See Fig. 1 for reference sequences.
http://vir.sgmjournals.org 1305
Phylogenetic analysis of FIV
Downloaded from www.microbiologyresearch.org by
IP: 104.249.141.27
On: Wed, 27 Jul 2016 20:44:44
and recombination frequency would necessitate the analysis
of full-length genomes by analogy to the HIV-1 nomenclature
proposal (Robertson et al., 1999).
This work provides the first evidence that FIV of subtype B
is predominant and highly divergent in Austria. Each of
the described Austrian clusters within clade B consists of
strains derived from different provinces of Austria (Table 1).
Moreover, strains from the same provinces group into
different subclades. Therefore these clusters represent real
subclades rather than artefacts based on a common origin
of the cats. Only a single subtype A strain was detected
in Austria. In contrast, subtype A seems to occur more
frequently in Germany. Our findings are in accordance with
work by other groups, who found clade A and less frequ-
ently, clade B strains in Germany (Bachmann et al., 1997)
and a high prevalence of clade B FIV in Italy (Pistello et al.,
1997). However, more detailed screening studies would
be necessary to precisely determine the prevalence of the
occurring subtypes in Austria and Germany. The success
of a vaccine might be largely dependent on the type and
variety of circulating strains, which can differ substantially
from region to region. In the light of the first commercial
FIV-vaccine, it is even more important to consider the
existing variety beforehand to prevent vaccination failure.
Likewise, as new PCR-based diagnostic tools gain impor-
tance in the fields of diagnostics and research, knowledge
about the genetic diversity and the compilation of new
sequence data provide a valuable tool for the design of
sensitive assays.
ACKNOWLEDGEMENTS
We thank Christina Musil, Katrin Hartmann, Christiane Stengel,
Werner Mu
¨ller, Ernst Leidinger and Angela Meyer for providing FIV-
positive blood samples and Brian Salmons for critical reading of the
manuscript. This work was supported by a research fund from the
Austrian Ministry for Education, Science and Culture.
REFERENCES
Bachmann, M. H., Mathiason-Dubard, C., Learn, G. H., Rodrigo,
A. G., Sodora, D. L., Mazzetti, P., Hoover, E. A. & Mullins, J. I. (1997).
Genetic diversity of feline immunodeficiency virus: dual infection,
recombination, and distinct evolutionary rates among envelope
sequence clades. J Virol 71, 4241–4253.
Bendinelli, M., Pistello, M., Lombardi, S., Poli, A., Garzelli, C.,
Matteucci, D., Ceccherini-Nelli, L., Malvaldi, G. & Tozzini, F. (1995).
Feline immunodeficiency virus: an interesting model for AIDS
studies and an important cat pathogen. Clin Microbiol Rev 8, 87–112.
Bigornia, L., Lockridge, K. M. & Sparger, E. E. (2001). Construction
and in vitro characterization of attenuated feline immunodeficiency
virus long terminal repeat mutant viruses. J Virol 75, 1054–1060.
Cammarota, G., Da Prato, L., Nicoletti, E., Matteucci, D., Bendinelli,
M. & Pistello, M. (1996). Quantitation of feline immunodeficiency
proviruses in doubly infected cats using competitive PCR and a
fluorescence-based RFLP. J Virol Methods 62, 21–31.
Carpenter, M. A., Brown, E. W., MacDonald, D. W. & O’Brien, S. J.
(1998). Phylogeographic patterns of feline immunodeficiency virus
genetic diversity in the domestic cat. Virology 251, 234–243.
Elyar, J. S., Tellier, M. C., Soos, J. M. & Yamamoto, J. K. (1997).
Perspectives on FIV vaccine development. Vaccine 15, 1437–1444.
English, R. V., Nelson, P., Johnson, C. M., Nasisse, M., Tompkins,
W. A. & Tompkins, M. B. (1994). Development of clinical disease in
cats experimentally infected with feline immunodeficiency virus.
J Infect Dis 170, 543–552.
Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a
maximum likelihood approach. J Mol Evol 17, 368–376.
Fitch, W. M. (1977). On the problem of discovering the most
parsimonious tree. Am Nat 111, 223–257.
Graur, D. & Li, W.-H. (2000). Fundamentals of molecular evolution,
2nd edn. Edited by A. D. Sinauer & C. J. Wigg. Sunderland, MA:
Sinauer Associates.
Hosie, M. J., Osborne, R., Yamamoto, J. K., Neil, J. C. & Jarrett,
O. (1995). Protection against homologous but not heterologous
challenge induced by inactivated feline immunodeficiency virus
vaccines. J Virol 69, 1253–1255.
Hosie, M. J., Flynn, J. N., Rigby, M. A. & 9 other authors (1998).
DNA vaccination affords significant protection against feline
immunodeficiency virus infection without inducing detectable
antiviral antibodies. J Virol 72, 7310–7319.
Hosie, M. J., Willett, B. J., Klein, D., Dunsford, T. H., Cannon, C.,
Shimojima, M., Neil, J. C. & Jarrett, O. (2002). Evolution of
replication efficiency following infection with a molecularly cloned
feline immunodeficiency virus of low virulence. J Virol 76, 6062–
6072.
Kakinuma, S., Motokawa, K., Hohdatsu, T., Yamamoto, J. K.,
Koyama, H. & Hashimoto, H. (1995). Nucleotide sequence of feline
immunodeficiency virus: classification of Japanese isolates into two
subtypes which are distinct from non-Japanese subtypes. J Virol 69,
3639–3646.
Klein, D., Janda, P., Steinborn, R., Muller, M., Salmons, B. &
Guenzburg, W. H. (1999). Proviral load determination of different
feline immunodeficiency virus isolates using real-time polymer-
ase chain reaction: influence of mismatches on quantification.
Electrophoresis 20, 291–299.
Klein, D., Leutenegger, C. M., Bahula, C., Gold, P., Hofmann-
Lehmann, R., Salmons, B., Lutz, H. & Guenzburg, W. H. (2001).
Influence of preassay and sequence variations on viral load deter-
mination by a multiplex real-time reverse transcriptase-polymerase
chain reaction for feline immunodeficiency virus. J Acquir Immune
Defic Syndr 26, 8–20.
Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001). MEGA2:
molecular evolutionary genetics analysis software. Bioinformatics 17,
1244–1245.
Leutenegger, C. M., Klein, D., Hofmann-Lehmann, R., Mislin, C.,
Hummel, U., Bo
¨ni, J., Boretti, F., Guenzburg, W. H. & Lutz, H. (1999).
Rapid feline immunodeficiency virus provirus quantitation by
polymerase chain reaction using the TaqMan fluorogenic real-time
detection system. J Virol Methods 78, 105–116.
Lockridge, K. M., Chien, M., Dean, G. A., Stefano Cole, K.,
Montelaro, R. C., Luciw, P. A. & Sparger, E. E. (2000). Protective
immunity against feline immunodeficiency virus induced by
inoculation with vif-deleted proviral DNA. Virology 273, 67–79.
Lole, K. S., Bollinger, R. C., Paranjape, R. S., Gadkari, D., Kulkarni,
S. S., Novak, N. G., Ingersoll, R., Sheppard, H. W. & Ray, S. C.
(1999). Full-length human immunodeficiency virus type genomes
from subtype C-infected seroconverters in India, with evidence of
intersubtype recombination. J Virol 73, 152–160.
1306 Journal of General Virology 84
A. Steinrigl and D. Klein
Downloaded from www.microbiologyresearch.org by
IP: 104.249.141.27
On: Wed, 27 Jul 2016 20:44:44
Matteucci, D., Pistello, M., Mazzetti, P., Giannecchini, S., Del Mauro,
D., Zaccaro, L., Bandecchi, P., Tozzini, F. & Bendinelli, M. (1996).
Vaccination protects against in vivo-grown feline immunodeficiency
virus even in the absence of detectable neutralizing antibodies. J Virol
70, 617–622.
Pecoraro, M. R., Tomonaga, K., Miyazawa, T., Kawaguchi, Y.,
Sugita, S., Tohya, Y., Kai, C., Etcheverrigaray, M. E. & Mikami, T.
(1996). Genetic diversity of Argentine isolates of feline immuno-
deficiency virus. J Gen Virol 77, 2031–2035.
Pedersen, N. C., Yamamoto, J. K., Ishida, T. & Hansen, H. (1989).
Feline immunodeficiency virus infection. Vet Immunol Immuno-
pathol 21, 111–129.
Pistello, M., Cammarota, G., Nicoletti, E., Matteucci, D., Curcio, M.,
Del Mauro, D. & Bendinelli, M. (1997). Analysis of the genetic
diversity and phylogenetic relationship of Italian isolates of feline
immunodeficiency virus indicates a high prevalence and hetero-
geneity of subtype B. J Gen Virol 78, 2247–2257.
Pu, R., Coleman, J., Omori, M., Arai, M., Hohdatsu, T., Huang, C.,
Tanabe, T. & Yamamoto, J. K. (2001). Dual-subtype FIV vaccine
protects cats against in vivo swarms of both homologous and
heterologous subtype FIV isolates. AIDS 15, 1225–1237.
Rigby, M. A., Holmes, E. C., Pistello, M., Mackay, A., Brown, A. J.
& Neil, J. C. (1993). Evolution of structural proteins of feline
immunodeficiency virus: molecular epidemiology and evidence of
selection for change. J Gen Virol 74, 425–436.
Robertson, D. L., Anderson, J. P., Bradac, J. A. & 17 other authors
(1999). HIV-1 nomenclature proposal. http://hiv-web.lanl.gov/
content/hiv-db/REVIEWS/reviews.html
Saitou, N. & Nei, M. (1987). The neighbor-joining method: a
new method for reconstructing phylogenetic trees. Mol Biol Evol
4, 406–425.
Salminen, M. O., Carr, J. K., Burke, D. S. & McCutchan, F. E. (1995).
Identification of recombination breakpoints in HIV-1 by boot-
scanning. AIDS Res Hum Retroviruses 11, 1423–1425.
Sodora, D. L., Shpaer, E. G., Kitchell, B. E., Dow, S. W., Hoover,
E. A. & Mullins, J. I. (1994). Identification of three feline
immunodeficiency virus (FIV) env gene subtypes and comparison
of the FIV and human immunodeficiency virus type 1 evolutionary
patterns. J Virol 68, 2230–2238.
Strimmer, K. & von Haeseler, A. (1996). Quartet puzzling: a quartet
maximum likelihood method for reconstructing tree topologies. Mol
Biol Evol 13, 964–969.
Strimmer, K. & von Haeseler, A. (1997). Likelihood mapping: a
simple method to visualize phylogenetic content of a sequence
alignment. Proc Natl Acad Sci U S A 94, 6815–6819.
Swofford, D. L. (2002). PAUP*. Phylogenetic Analysis Using
Parsimony (*and other methods). Version 4.0b10. Sunderland,
MA: Sinauer Associates.
Swofford, D. L., Olsen, G. J., Waddell, P. J. & Hillis, D. M. (1996).
Phylogenetic inference. In Molecular Systematics, 2nd edn,
pp. 407–543. Edited by D. M. Hillis, C. Moritz & B. K. Mable.
Sunderland, MA: Sinauer Associates.
Tamura, K. & Nei, M. (1993). Estimation of the number of nucleotide
substitutions in the control region of mitochondrial DNA in humans
and chimpanzees. Mol Biol Evol 10, 512–526.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. &
Higgins, D. G. (1997). The CLUSTAL X windows interface: flexible
strategies for multiple sequence alignment aided by quality analysis
tools. Nucleic Acids Res 25, 4876–4882.
Uhl, E. W., Heaton-Jones, T. G., Pu, R. & Yamamoto, J. K. (2002).
FIV vaccine development and its importance to veterinary and
human medicine: a review. FIV vaccine 2002 update and review. Vet
Immunol Immunopathol 90, 113–132.
Xia, X. & Xie, Z. (2001). DAMBE: data analysis in molecular biology
and evolution. J Hered 92, 371–373.
Yamamoto, J. K., Hohdatsu, T., Olmsted, R. A. & 7 other authors
(1993). Experimental vaccine protection against homologous and
heterologous strains of feline immunodeficiency virus. J Virol 67,
601–605.
http://vir.sgmjournals.org 1307
Phylogenetic analysis of FIV
