Genetics and Evolutionary Aspects
Hypothesis: SARS-associated Coronavirus is a separate genus from
other Coronavirus
-
It would seem that none of the publications on
SARS thus far included an outgroup in the phylogenetic trees
presented.
-
Lack of an outgroup means that the tree cannot
be rooted
-
An unrooted tree does not indicate the
direction of evolution, or the polarity of characters2
-
Thus, goals of this analysis is to:
a) discern the evolutionary relationship between SARS and
coronavirus by rooting the tree with torovirus as an outgroup;
b) the relative rate of mutation of SARS in relation to other
coronavirus, using Tajima's relative-rates test;
c) determine whether SARS is under positive selection pressure
by comparing the rates of synonymous versus nonsynomymous
mutations
-
Results from this analysis must be interpreted
in light of the host-virus relationship and interaction of
susceptible host with the environment in order to provide a more
coherent picture. Also, several assumptions and constraints have
been made in drawing these conclusions.
The nucleotide sequence of Urbani-SARS
coronavirus ORF1b RNA polymerase was obtained from the WHO
Collaborative Networks3. The nucleotide sequence was translated
to amino acid sequence (Figure 1). The translation was verified with
BLASTX (translated BLAST search - nucleotide query to protein db).
Nucleotide sequences of RNA-directed RNA polymerase from Canine coronavirus
UWSMN-1 (gi|22774013); Porcine transmissible gastroenteritis virus (gi|4927036);
Turkey coronavirus (gi|4927034); Rat sialodacryoadenitis coronavirus
(gi|4927032); Human coronavirus (strain OC43) (gi|4927030); Porcine
hemagglutinating encephalomyelitis virus (gi|4927028); Feline infectious
peritonitis virus (gi|4927026); Canine coronavirus (gi|4927024); Bovine
coronavirus (gi|4927022); and Breda torovirus (gi|4204756) were obtained from
NCBI nucleotide database. The sequences were aligned using the program
ClustalW 1.81 (ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw) with default
parameters (gap opening penalty=10, gap extension penalty=0.20). The alignments
were then formatted to a MEGA format. The alignments were visualized in MEGA
version 2.1 (Kumar et al. 2002). A preliminary phylogenetic tree was constructed
with the following method in place:
Unweighted Pair Group Method with Arithmetic mean (UPGMA), Kimura 2-parameter,
and bootstrap with 100 replications. Tajima relative-rate tests are
then performed between SARS-associated coronavirus, Bredavirus, and
coronavirus from all three antigenic groups.

Figure 2b: Traditional
Rectangular View

Figure 2c: Bootstrap Consensus Tree

Table 1: Pairwise
Distance between all viruses examined, using the Kimura 2-Parameter
method
|
PHEV
|
BCOV
|
OC43
|
RAT
|
TCOV
|
CCOV1
|
CCOV2
|
FIPV
|
PTGEV
|
SARS
|
BCOV
|
0.017
|
|
|
|
|
|
|
|
|
|
OC43
|
0.044
|
0.044
|
|
|
|
|
|
|
|
|
RAT
|
0.132
|
0.116
|
0.121
|
|
|
|
|
|
|
|
TCOV
|
0.436
|
0.452
|
0.428
|
0.452
|
|
|
|
|
|
|
CCOV1
|
0.436
|
0.436
|
0.483
|
0.445
|
0.504
|
|
|
|
|
|
CCOV2
|
0.444
|
0.452
|
0.484
|
0.445
|
0.513
|
0.040
|
|
|
|
|
FIPV
|
0.429
|
0.436
|
0.484
|
0.446
|
0.530
|
0.045
|
0.049
|
|
|
|
PTGEV
|
0.436
|
0.444
|
0.475
|
0.445
|
0.511
|
0.049
|
0.045
|
0.040
|
|
|
SARS
|
1.036
|
1.091
|
1.165
|
1.204
|
1.357
|
1.017
|
1.164
|
1.091
|
1.108
|
|
BREDA
|
1.480
|
1.480
|
1.589
|
1.767
|
1.906
|
1.862
|
1.749
|
1.879
|
1.624
|
1.477
|
Average
Pairwise Distance between the Three Antigenic Groups and
SARS-associated Coronavirus:
I
and II
|
0.429
to 0.484
|
I
and III
|
0.504
to 0.530
|
II
and III
|
0.428
to 0.452
|
SARS
and I
|
1.017
to 1.164
|
SARS
and II
|
1.036
to 1.204
|
SARS
and III
|
1.357
|
Viruses
within the coronavirus family separate into three antigenic groups as
expected. However, the genetic distance between SARS and other
coronaviruses is similar to the distance between SARS and Bredavirus
but different from the distance between coronaviruses from all three
antigenic groups (see the above table). This is something not found in
other publications on SARS thus far. This, in conjunction with the UPGMA
tree obtained, seems to suggest that the SARS-associated coronavirus
diverged very early in the evolution from the ancestors of
coronavirus, soon after the divergence of Bredavirus (a torovirus
subfamily) from its common ancestor. Preliminary results from Tajima
relative-rates test between SARS-associated coronavirus, Bredavirus,
and coronavirus from all three antigenic groups suggest that the
SARS-associated coronavirus mutated at the same rate as other
coronaviruses. This decreases the likelihood that the
SARS-associated coronavirus is mutating faster than expected. These
results suggest that perhaps the new virus is a separate genus distinct from
other known coronavirus.
-
complete the Tajima's relative-rate
test
-
construct phylogenetic trees using
other methods, like maximum parsimony, minimum evolution
-
use more than one outgroup in the
construction of the trees, such as including Arterivirus
-
repeat the experiment with other
genes in the SARS-associated coronavirus
|