Fig 1.
Sample sources and number of DuCV-positive samples.
Different background colors represent different numbers of sample sources; the size of th e circles indicates the number of DuCV-positive samples, with specific quantities marked in the graph. The boundary data for China's provincial-level administrative divisions were obtained from the Resource and Environment Science Data Platform (https://www.resdc.cn/).
Fig 2.
DuCV detected from January to October 2022.
(A) Number and percentage of DuCV-positive samples identified each month from January to October; (B) Distribution of the number of DuCV-positive samples relative to the number of day-old DuCV-infected ducks.
Fig 3.
Numbers and positive rates of mixed infection with DuCV and other viruses or bacteria in ducks.
NGPV: novel goose parvovirus, MDPV: Muscovy duck parvovirus, RA: Riemerella anatipestifer, DAstV: duck astrovirus, PM: Pasteurella multocida, DHAV: duck hepatitis A virus, DRV: duck reovirus, NDRV: novel duck reovirus, AIV: avian influenza virus, DTMUV: duck Tembusu virus, DEV: duck enteritis virus, CP: Clostridium perfringens, FAdV: fowl adenovirus.
Fig 4.
DuCV genetic evolutionary tree based on the full-length genome.
All full-length gene sequences of DuCV prior to 2023 were downloaded from NCBI, and a phylogenetic tree was constructed with the 51 DuCV sequences identified in this study. The different colors in the inner circles represent different genotypes. The different colors in the outer circles represent different years. The red dots represent the DuCVs obtained in the present study. The red five-pointed stars represent the DuCV strains detected in China in different years.
Table 1.
Identity or distance of nucleotide and amino acid sequences within and between different genotypes in the present study.
Table 2.
Glycosylation and phosphorylation of some amino acid sites in the Cap protein of DuCV-1b.
Fig 5.
Mutation of amino acids in OPF2 was detected in all the sequenced strains in this study.
The top numbers represent amino acid positions. The dots in the figure represent the same amino acids as those in reference strain AY228555.1.
Fig 6.
ORF2 genetic evolution analysis of DuCV-1b.
The external ribbon represents amino acids at different positions.
Fig 7.
Tertiary structure of the Cap protein predicted via Phyre2 (confidence in the model: 100%).
(A) and (B) Positions of the 5 variable regions; the reference sequences for both graphs are those of AY228555.1. The amino acids at positions 3–15 are not included the protein's tertiary structure. (C) Positions of some amino acids and the changes in protein shape due to gene mutations.
Table 3.
Partial recombination events detected in the present study.
Fig 8.
Presentation of recombination events with Simplot.
(A) Recombination event 1. (B) Recombination event 7.
Fig 9.
Phylogenetic trees illustrating the potential recombination events shown in Fig 8. The nucleotide positions are consistent with the breakpoint positions in Table 3, representing the aligned positions following sequence alignment, not the original sequence positions.
For event 1 (A–C), the nucleotide sequence positions are 1–943, 944–1084, and 1085–1903; for event 7 (D–F), the nucleotide sequence positions are 1–979, 980–1402, and 1403–1903. The breakpoint locations represent the boundaries of the strongest recombination signal but are not necessarily close to the locations of the failures that occurred in the original recombination event.
Table 4.
PCR primers for detection and DuCV genome amplification.