1. Introduction
Waterfowl parvoviruses are highly contagious, lethal pathogens for goslings and ducklings. Waterfowl parvoviruses belong to the species
Anseriform dependoparvovirus 1 of the genus
Dependoparvovirus within the
Parvoviridae family. The genus
Dependoparvovirus can be divided into two divergent groups, consisting of Muscovy duck parvovirus (MDPV)-related groups and goose parvovirus (GPV)-related groups [
1]. GPV, the agent of Derzy’s disease, causes the disease in young geese and Muscovy ducks with mortality rates up to 90% [
2], while MDPV causes high mortality, watery diarrhea, wheezing, locomotor dysfunction, and stunning in Muscovy ducks [
3]. Both GPV and MDPV can show 70–100% morbidity and mortality during the first 3–4 weeks of age.
Waterfowl parvovirus is characterized as a non-enveloped virus. The viral genome consists of a single-strand DNA with around 5100 bp. The translated regions contain two open reading frames (ORFs). The left ORF encodes for the non-structural protein, while the remaining ORF encodes for capsid proteins VP1, VP2, and VP3 [
4,
5]. Both GPV and MDPV are antigenically related to each other as they share about 85% protein sequence homology [
6]. In detail, they show nucleotide differences in VP1 of about 20–24%, whereas these differences in VP1 within the GPV and MDPV groups are only 0.1–7% and 0.1–1.9%, respectively [
6,
7,
8,
9].
It was reported that recombination events occurred among parvoviruses. As a result, a novel strain may be generated from the recombination event between vaccine and wild-type strains [
10]. In 2015, Chen et al. found a novel goose parvovirus (NGPV) causing a severe disease in duck flocks in China [
11]. Later, other studies noted that NGPV strains induced short beak and dwarfism syndrome (SBDS) in China, Egypt, and Poland [
12,
13,
14]. NGPV viruses were considered to derive from classical GPV strains. Furthermore, a novel recombinant MDPV (rMDPV) was reported in ducks from several provinces in mainland China, where it caused high mortality and embolism in the intestinal tracts of infected ducklings aged less than 3 weeks [
15,
16,
17].
In Vietnam in 2019, waterfowl parvoviruses have been reported in sick ducks with short beak and dwarfism syndrome. The detected waterfowl parvovirus was genetically grouped with the NGPV group based on the partial NS and VP1 genes [
18]. However, information on waterfowl parvoviruses has been limited up to now. Therefore, we investigated infections of waterfowl parvoviruses in ducks farmed in some provinces of northern Vietnam. The current study also carried out molecular characterization of the near-complete waterfowl parvovirus genome.
4. Discussion
Understanding waterfowl parvovirus infections is important as they are associated with SBDS in ducks with a high or low mortality [
12,
13,
14]. Recently, waterfowl parvoviruses were characterized based on partial sequences of the VP1 and NS1 gene sequences and divided into the NGPV group in Hungyen province [
18]. The Vietnamese waterfowl parvovirus genome sequences are still limited in GenBank; additional sequence data of the complete genome are necessary to further characterize and understand the evolution of viral strains. This was the first study to conduct epidemiological analysis and to further characterize the whole-genome sequences (4880 bp) of Vietnamese waterfowl parvovirus strains.
In the current study, the waterfowl parvovirus genome was detected in 20% of duck samples, which was lower than that of ducklings from outbreak farms with SBDS in tissue samples (33/33 (100%)) or with no clinical signs (7/12 (58.33%)) [
24]. The differences in the sampling numbers, location, time, and sensitivity of the detection methods were considered a reasonable cause for the variation in the result. Furthermore, 36.84% of the duck farms were positive for the viral genome in northern provinces in Vietnam. The current results suggested that waterfowl parvovirus may circulate and affect duck production in Vietnam. In the current study, we first found a moderate waterfowl parvovirus genome frequency of detection in Vietnamese ducks at age 2–4 weeks (37.04%), with the frequency of detection of viral genome higher than that in younger ducks aged <2 weeks (9.09%) and older ducks aged >4 weeks (16.30%). These findings suggested that during age 2–4 weeks the ducklings may be susceptible to viral infection.
Genetic and phylogenetic analyses indicated that the Vietnamese and Chinese strains were clustered in a single genogroup belonging to NGPV (
Figure 2,
Figure 3 and
Figure 4). The results suggested that these viruses may have a similar origin, or that these viruses were widespread in Asia. In addition, the classification of the Vietnamese NGPV sequences was similar based on the complete genome, Rep gene, and Cap gene sequences, suggesting that using each gene sequence could characterize the viral strains. Amino acid substitutions on Rep and Cap proteins play critical roles in the change of host range and pathogenicity. In terms of Rep protein, a previous study reported that substitution at residue 140 (A to S), which was not be found in the current four Vietnamese strains, was associated with viral transcription [
25]. Yu et al. noted that five substitutions at residues 494, 553, 555, 573, and 594 on Rep protein play roles in the antigenic epitopes of B cells [
26]. Only one substitution at residue 555 N/D to P/T was detected in the present study. The roles of the remaining three substitutions on Rep protein of the Vietnamese strains were still unclear. In this study, 14 substitutions on Cap protein did not match with residues 35 and 660, which may be related to the host range identification of NGPV [
27].
SBDS was recognized in the NGPV group in China in 2015 [
11]. Since then, this pathogen has been critical in causing disease in ducks, mainly in China but also in other countries. In the current study, the four NGPVs were detected based on their complete genome sequences. The four Vietnamese NGPVs obtained were closely related to NGPV in China in 2019 (HuN18). The HuN18 NGPV virus has been isolated from ducks with BADS in China [
28]. Therefore, it could be speculated that the current Vietnamese NGPV strains may be high-virulence strains.
Recombination has been reported in the evolutionary processes of waterfowl parvoviruses and described [
17,
28,
29,
30] based on the complete genome sequences. A recombination event may generate a novel waterfowl parvovirus strain [
10]. The current study revealed the first evidence supporting a recombination event in the Vietnamese NGPV strain in the protein-coding region of the Capsid gene. In general, recombination usually occurs between viruses that are located closely to each other. However, the major and minor parents were from China. The explanation for this situation is that Vietnam and China share thousands of kilometers along their border. The recombination event could have occurred elsewhere in China and then could have been transferred to Vietnam through daily trading of live birds along the border between Vietnam and China [
31]. Recombination may occur between the Vietnamese waterfowl parvovirus strains, which might be detected if there are sufficient data. Analysis of the additional viral genomes should be further studied.
Another evolutionary process is natural selection. Fan et al. [
32] reported nine sites on VP protein that were estimated as positively selected sites, that may have been associated with host range [
32]. In the current study, only one positive selection on a VP protein was found (residue 507), which has not been characterized. Further studies should be conducted to clarify this point.