The complete mitochondrial sequence of 17,030 bp was obtained from Echinostoma revolutum and characterized with those of previously reported members of the superfamily Echinostomatoidea, i.e. six echinostomatids, one echinochasmid, five fasciolids, one himasthlid, and two cyclocoelids. Relationship within suborders and between superfamilies, such as Echinostomata, Pronocephalata, Troglotremata, Opisthorchiata, and Xiphiditata, are also considered. It contained 12 protein-coding, two ribosomal RNA, 22 transfer RNA genes and a tandem repetitive consisting non-coding region (NCR). The gene order, one way-positive transcription, the absence of atp8 and the overlapped region by 40 bp between nad4L and nad4 genes were similar as in common trematodes. The NCR located between tRNAGlu (trnE) and cox3 contained 11 long (LRUs) and short repeat units (SRUs) (seven LRUs of 317 bp, four SRUs of 207 bp each), and an internal spacer sequence between LRU7 and SRU4 specifying high-level polymorphism. Special DHU-arm missing tRNAs for Serine were found for both tRNAS1(AGN) and tRNAS2(UCN). Echinostoma revolutum indicated the lowest divergence rate to E. miyagawai and the highest to Tracheophilus cymbius and Echinochasmus japonicus. The usage of ATG/GTG start and TAG/TAA stop codons, the AT composition bias, the negative AT-skewness, and the most for Phe/Leu/Val and the least for Arg/Asn/Asp codons were noted. Topology indicated the monophyletic position of E. revolutum to E. miyagawai. Monophyly of Echinostomatidae and Fasciolidae was clearly solved with respect to Echinochasmidae, Himasthlidae, and Cyclocoelidae which were rendered paraphyletic in the suborder Echinostomata.

A single-step multiplex PCR (here referred to as a duplex PCR) has been developed for simultaneous detection and diagnosis of Fasciola hepatica and F. gigantica. These species overlap in distribution in many countries of North and East Africa and Central and Southeast Asia and are similar in egg morphology, making identification from fecal samples difficult. Based on a comparative alignment of mitochondrial DNA (mtDNA) spanning the region of cox1-trnT-rrnL, two species-specific forward primers were designed, FHF (for F. hepatica) and FGF (for F. gigantica), and a single reverse primer, FHGR (common for both species). Conventional PCR followed by sequencing was applied using species-specific primer pairs to verify the specificity of primers and the identity of Fasciola DNA templates. Duplex PCR (using three primers) was used for testing with the DNA extracted from adult worms, miracidia, and eggs, producing amplicons of 1,031 bp for F. hepatica and 615 bp for F. gigantica. The duplex PCR failed to amplify from DNA of other common liver and intestinal trematodes, including two opisthorchiids, three heterophyids, an echinostomid, another fasciolid, and a taeniid cestode. The sensitivity assay showed that the duplex PCR limit of detection for each Fasciola species was between 0.012 ng and 0.006 ng DNA. Evaluation using DNA templates from 32 Fasciola samples (28 adults and 4 eggs) and from 25 field-collected stools of ruminants and humans revealed specific bands of the correct size and the presence of Fasciola species. This novel mtDNA duplex PCR is a sensitive and fast tool for accurate identification of Fasciola species in areas of distributional and zonal overlap.

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Introduction: The aim of this study was to identify the genetic characteristics and molecular genotyping of duck hepatitis A virus (DHAV) isolated in Vietnam during [2009][2010][2011][2012][2013]. Methodology: Thirty duckling livers from outbreaks between 2009 and 2013 in seven provinces were collected and identified by polymerase chain reaction (PCR). Then, VP1 genes of eleven positive samples and two attenuated vaccine strains were sequenced and analyzed. Results: Genotypic and phylogenetic analyses indicated that the 13 Vietnamese isolates were classified into two genotypes, DHAV-1 and DHAV-3. The rate of identity and homology was 91%-100% between the 10 Vietnamese and 26 global strains of DHAV-3, and 92%-100% between 3 Vietnamese and 16 strains of DHAV-1. Between the DHAV-3 and DHAV-1 strains, the divergence reached 30%. At the C-terminal of VP1 for the different strains, a hypervariable region was observed, and notably, six of the Vietnamese DHAV-3 strains in this study showed four consistent differences (at positions T184M, Q200H, K207N, and K214R) within this group that were distinct from all other DHAV-3 strains. Conclusions: This is the first report of molecular characterization of DHAVs in Vietnam. At least two genotypes were identified, DHAV-1 and DHAV-3, with diversified clades within and between genotypes. DHAV-3 seemed to be dominant in Vietnam.

Eight Vietnamese Newcastle disease virus field isolates from 2008-2015 and 3 vaccine specimens were genotyped based on their full F gene sequences and compared to 80 reference strains representing all 18 genotypes. Three isolates formed a novel subgenotype XIId, identified for the first time in Vietnam; while the others clustered as follows: four in subgenotypes VIId and VIIh; two in Genotype I; and two in Genotype II. Evolutionary distance calculations confirmed the Vietnamese XIId isolates were distinct from XIIa and XIIb by 0.062-0.070; and from other genotypes by 0.089-0.245. This data demonstrated that a novel XIId subgenotype emerged in Vietnam indicating considerable genetic diversity, thus highlighting the need to implement antigenic matching during vaccination against NDVs.

The complete sequence for viral protein 2 (VP2) of canine parvovirus (CPV) was obtained from 33 isolates collected from dogs with clinical symptoms and a vaccine in Vietnam from Mar 2017-June 2019. Molecular analysis revealed the descent evolution in CPV-2c-"new", forming a "new var." sublineage of the substantial 5G, 447M mutations restricted to the Vietnamese isolates in the epitope stretches. These were found besides the common 80R,

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The unified genotypic classification scheme (genotypes A0, A1–A8, and B1–B5) was proposed and applied for the classification of the infectious bursal disease virus (IBDV). Since 1987, IBDVs have circulated and evolved in Vietnam, but little is known about the genotypes present. The IBDV samples were collected in 1987, 2001–2006, 2008, 2011, 2015–2019, and 2021 in 18 provinces. We conducted phylogenotyping analysis based on the alignment of 143 VP2-HVR (439 bp, nt 628–1066; aa 210–355 in VP2), including 64 Vietnamese isolates and two vaccines, and 82 VP1 B-marker (725 bp, nt 13–737; aa 4–245 in VP1) sequences, including four Vietnamese isolates and one vaccine. The analysis revealed three A-genotypes, A1, A3, and A7, and two B-genotypes, B1 and B3, among the Vietnamese IBDVs. The IBDV strains showed the lowest average evolutionary distance at 8.6% between A1 and A3 and the highest (21.7%) between A5 and A7, while 14% was between B1 and B3 and 17% between B3 and B2. The signature residues 222T - 253Q - 256V - 294L - 299(S/N) appeared to be unique for the genotype A2; the 222A - 253Q - 256I - 294I - 299S for the A3, the 222T - 253Q - 256V - 294L - 299N for the A5, the 222Q - 253E - 256K - 294L - 299S for the A6, and the 222A - 253Q - 256A - 294L - 299S for the A8, and each of these could be the genotypical motif for genotypic discrimination. The timeline statistical summary revealed that the A3-genotype predominated (79.8% presence) in Vietnam from 1987 to 2021 and that it has remained dominant in circulating IBDVs over the last five years (2016–2021).