3.3 Analysis of nucleotide sequence of cap gene and amino
acid sequence of the cap protein
To explore the genetic relationship and evolution of PiCV from 2016 to
2019, the cap genes of 90 PiCV strains of the 120 PiCV positive
samples were successfully sequenced. Detailed information on the 90 PiCV
strains is shown in Table 2 and S1. The cap gene of 90 samples
obtained in this study were used to compare with reference sequences
from the Chinese and the other countries PiCV reference strains. The
results showed that the cap gene of all 90 strains was ranging
from 813 to 828 nt in length. Fourteen, thirteen, one, fifty-three,
seven, and two of the 90cap nucleotide sequences
were 813 nt, 816 nt, 819 nt, 822 nt, 825 nt, and 828 nt in length,
encoding a cap protein of 270, 271, 272, 273, 274, and 275 amino
acid residues, respectively (Table 2 and S1). The sequence comparison of
the cap genes revealed nucleotide homologies of 71.9%–100% and
deduced amino acid homologies of 71.7%–100% among the 90 PiCV
strains. The cap genes of the 90 identified PiCV strains
exhibited low sequence similarities with Chinese PiCV reference strains
(73.0%–99.6% nucleotide identity, 72.3%–100% amino acid identity)
and the PiCV reference strains from the other countries (68.8%–98.4%
nucleotide identity, 63.6%–100% amino acid identity) (Table 3).
Analysis of nucleotide sequences in the cap gene fragment
indicated the appearance of many mutations. The strains identified in
this study were formed into four groups (ATG (n=80), ATA (n=6), ATT
(n=2), and GTG (n=2)) as the result of the mutation at the initiation
codons (Table 2 and S1). To investigate variations in the deduced amino
acid sequences of cap gene products, the amino acid sequences of
90 cap proteins and the reference strains were aligned. The
results showed that there are nine major locations of deletions
(compared to the consensus sequence) among the cap proteins.
These include locations 7, 24, 29, 30, 35, 58, 130, 182, and 266 (Figure
1).
A
comparison of entropy (Hx) in amino acid sequences of capproteins showed that the Hx of amino acid sequences at most positions
from the 90 identified PiCV strains were higher than that of the PiCV
reference strains (Figure 2). In addition, some unique amino acid
substitutions at 28 different positions were observed among thecap proteins of 90 identified PiCV strains as shown in Table 4
and Figure 3.