Classical swine fever (CSF) is a major pig disease worldwide (1). Some research studies
have focused on developing new control policies, especially for CSF-endemic countries.
A recent study by Yoo et al. (2) described the genetic evolution of CSF virus (CSFV)
under immune environments conditioned by genotype 1-based modified live virus vaccine
(MLV). Based on their results, the authors suggest there is a need to develop a new
CSFV vaccine based on CSFV-genotype 2 (CSFV-G2) (2). However, as discussed below,
the main findings of this study were not properly supported by the results or by the
choice of experimental design.
Analyzing the global evolutionary patterns for CSFV, Yoo et al. (2) stated that the
genetic diversity of the CSFV-G2 was higher than that of the CSFV-genotype 1 (CSFV-G1).
In this experiment, the authors compared the effective population size (Ne) vs time
between both genotypes (2). The authors suggest that the Ne values for the CSFV-G1
remained relatively constant whereas, for CSFV-G2, the Ne values gradually expanded
after 1980 (2). However, by looking at the effective population size (y-axis), it
is clear that the Ne for CSFV-G1 was higher (around 102–2.5) compared to the Ne values
of CSFV-G2 until the year 2000. Between 2000 and 2005, there is a sudden increase
in the Ne for CSFV-G2 followed by an almost equal decrease. The Ne values remain higher
for CSFV-G1 compared to CSFV-G2, plateauing at approximately 102.5 after 2009 at the
time when the genetic diversity of the CSFV-2 continues to decrease. Moreover, any
comparison after this point is difficult to assess since the authors did not continue
their analysis for CSFV-G1 after 2010, unlike that of CSFV-G2 (2). This raises an
additional concern regarding the inconsistency of this study, since CSFV-G1 sequences
collected after 2010 are available on GenBank databases and have been used in phylodynamic
studies for CSFV-G1 (3–5). Finally, in Figure 3, the genetic diversity is expressed
by the median estimate of the Ne (solid line) with a 95% highest posterior density
(HPD) interval (gray area) (2). Considering the 95% HPD, there is no statistical difference
between these two populations. From our analysis, the fact that the genetic diversity
of CSFV-G1 showed higher values than CSFV-G2 consistently over a longer period of
time (2) is an indication that CSFV-G1 has higher diversification than CSFV-G2, contradicting
the conclusions made by the authors.
Second, the author’s state: “CSFV-G2 has a more advantageous E2 codon composition
than CSFV-G1, in terms of survival in immune environments that have been optimally
created by CSFV genotype 1-based vaccination.” This conclusion was not supported by
the methods used. For the evaluation of the selective pressure on CSFV, Yoo et al.
(2) employed the estimation of the ratio of non-synonymous to synonymous substitution
rates using four different testing methods implemented in HYPhy package. However,
these methods were designed to determine the action of the evolutionary forces on
codon sites, but not to compare evolutionary advantages between lineages. Currently,
the only program to evaluate evolutionary advantages between lineages is PAML, since
branch-site models are implemented in this program (6). For this reason, the interpretation
of the results by Yoo et al. (2) was not properly supported. Alternatively, Rios et
al. (5) showed, using a branch-site model, that the only CSFV lineage selected by
positive selection was subgenotype 1.4 (5). When using this same model at the genotype
level, no evidence of evolutionary advantage by the action of positive selection pressure
for any of the CSFV genotypes assessed was observed (5).
Because of the emergence of neutralization-escape mutants from the CSFV-G2 strains
caused by the disproportionate use of MLV based on CSFV-G1, Yoo et al. (2) proposed
that there is a need to develop a new CSFV vaccine based on CSFV-G2 to prevent vaccine-escaping
mutants of this genotype. However, no experimental designs supporting this statement
were included in this study. Yoo et al. (2) restricted their study to describe some
amino acid substitutions found in the analyzed sequences. Based on these substitutions,
the authors conclude these are neutralization-escape mutants. Experiments using monoclonal
or polyclonal antibodies would have provided the necessary information to claim these
mutants were indeed neutralization-escape mutants.
A series of studies (3, 7–9) previously demonstrated the emergence of a neutralization-escape
mutant for CSFV strains from the subgenotype 1.4. In Perez et al. (3), the authors
found that the vaccination policy implemented in Cuba (CSF-endemic) led to a bottleneck
effect on the viral population in this country, causing the emergence of new strains.
Further studies revealed that one of the strains suggested to be a neutralization-escape
mutant showed lower virulence compared to the parental strain (7, 8) and induced postnatal
persistent infection, representing an evolutionary advantage (8). Coronado et al.
(9) compared the antigenic relationships between the parental strain that circulated
in Cuba (“Margarita strain”) and the new emergent strain (“Pinar del Rio”), as well
the capacity of neutralization induced by the MLV implemented in Cuba for both these
CSFV strains (9). The results from these studies showed antigenic differences between
the parental strain and the emergent strain when values of neutralization antibodies
(homologous and heterologous) were compared. Furthermore, whereas the immune response
induced by the MLV vaccine applied in Cuba was able to completely neutralize the parental
strain “Margarita,” it was only able to partially reduce the emergent strain “Pinar
del Rio” (9). This provides evidence that the MLV based on CSFV-G1 can induce neutralizing-escape
mutants in the same genotype due to positive selection pressure. It is probable that
the MLV based on CSFV-G1 1 could also induce the emergence of neutralizing-escape
mutants in the CSFV-G2, however, the study published by Yoo et al. (2) did not show
any evidence in this regard.
Relevant factors that could facilitate the emergence neutralization-escape mutants
for CSFV were omitted in Yoo et al. (2). These include: the composition of the quasispecies
cloud (10), the circulation of immunosuppressive (11), and the properties of the vaccine
(quality, doses, gaps in the cold chain) (1). Therefore, the suggestion to produce
a CSFV vaccine based on CSFV-G2 to avoid the emergence of neutralizing-escape mutants
of this genotype lacks sufficient supporting evidence.
Author Contributions
LR and LP wrote the manuscript. LP edited the manuscript. Both authors read and approved
the final version of the manuscript.
Conflict of Interest Statement
The authors declare that the research was conducted in the absence of any commercial
or financial relationships that could be construed as a potential conflict of interest.